ReSeqTools

A Toolkit for analyzing next-generation DNA Re-Sequencing data

Newest Reseqtools website 最新下载网址

https://github.com/BGI-shenzhen/Reseqtools




基于google在大陆被禁用和无法上传新的板本 最新板本请点击上面网页下载
https://github.com/BGI-shenzhen/Reseqtools

The paper (title: ReSeqTools?: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis )is here: 相关文章见下面： http://www.geneticsmr.com//year2013/vol12-4/pdf/gmr3109.pdf

硕士毕业文章Thesis Disseration Paper （Master）: http://cdmd.cnki.com.cn/Article/CDMD-10561-1013318279.htm 或者进入中国知网 http://www.cnki.net/ 搜： 基于重测序数据的群体SNP位点检测及基因型判断

http://www.cnki.net/KCMS/detail/detail.aspx?dbcode=CMFD&QueryID=0&CurRec=2&dbname=CMFDTEMP&filename=1013318279.nh&urlid=&yx=&v=MTIyNjNMdXhZUzdEaDFUM3FUcldNMUZyQ1VSTG1lWmVabUZpRG5VYjdCVkYyNkhiQzVGdFBMcHBFYlBJUjhlWDE=

Purposes

Introduction

iTools is a toolkit for analyzing next-generation DNA Re-Sequencing data.

Purposes

1) Provide an abundant toolkit for next-generation DNA Re-Sequencing analysis.

2) Save the storage space since it can also read and write compassion files.

3) Promote communication and together maintain the toolkit.

4) ...

Install

System Requirements Operating systems: Unix Programming language: C/C++ Other requirements: boost_1.44+ http://www.boost.org

Program had been included: zlib & libgzstream library, user can updata these two library. Compile and Install tar -zxvf iTools_Code20120522.tar.gz ; cd iTools_Code; make ; The iTools Toolkit and other related software are in the directory iTools_Code/bin .

For help messages in detail,please refer to iTools.Readme.pdf or use ./iTools -h

Usage

Fatools

```

1 Fatools Tools for file of FASTA format 1.1 stat quick stat fasta's info 1.2 findN quick find fasta's N region 1.3 extract get fragments from seq based on coordinates 1.4 regenerate merge a new Ref Bases scaffolds 1.5 filter filter the short & too many 'N' Seq 1.6 cutF cut fasta to fixed Num of subFile in total 1.7 cutS cut fasta to fixed Num of Seq in each subfile 1.8 getSP get Seq by specified ID or pattern 1.9 getSN get Seq by specified order Num range 1.10 getCdsPep get CDS Seq & Pep Seq based the gffFile 1.11 CDS2Pep Translate CDS-Seq to protein-Seq 1.12 reform reform/modify the sequence ```

Fqtools

2 Fqtools Tools for file of FASTQ format ```

2.1 stat quick stat fastq's info 2.2 filter filter fastq for clean datas 2.3 rmAdapterPE index rm adapter data filter of PE 2.4 rmAdapterSE index rm adapter data filter of SE 2.5 pooling pooling index library data filter ```

SOAPtools

3 SOAPtools Tools for file of mapping result SOAP format ```

3.1 split split soaplist by chr file 3.2 msort sort the SoapOut by chr and position 3.3 view view the Alignment of SoapBychrSort

3.4 merge merge multi SoapBychrSort to a Sort Soap 3.5 filter fiter/extract the soap Read 3.6 stat stat SortSoap of cov,depth,MisMacth... 3.7 rmdup remove PCR duplicates of SortSoap

3.8 genotype SortSoap--consistencygenotype,RST,Hit,Qseq... 3.9 Soap2Sam convert Soap 2 Sam Fomat 3.10 Xam2Soap convert Bam,Sam 2 Soap Fomat ```

CNStools

4 CNStools Tools for file of soapsnp result consensus . ```

Individual Usage: 4.1 ExtractCns Extract the potential snp from the cns file 4.2 FilterCns Filter the potential snp to get accurate SNP Population Usage: 4.3 GLFmulti Merge Glf(1.02) list to RawFile of Population 4.4 Addcn Add the copybernum for the RawFile

4.5 FilterRaw Filter Raw(+cp)Addcn file to get accurate Pop SNP 4.6 GLF2GPF Get the genotype from the glf List by Site 4.7 GLF2Geno Get the genotype from the glf List by Region 4.8 FilterGeno Filter genotype file to get accurate genotype SNP 4.9 MAF Stat Minor Allele Frequency in Raw or Addcn Tools Usage: 4.10 Fre Stat Row Frequency Distribution of file(List) 4.11 AddRef Add the Ref base to the InPut files 4.12 AddcnAll Add the copybernum for the RawFile

4.13 DepthGlf Stat the allele Depth distribution in glf(1.02) 4.14 DepthCns Stat the allele Depth Distribution in CNS 4.15 DepthRaw Stat allele Depth Distribution in Raw or Addcn ```

Xamtools

5 Xamtools Tools for file of mapping result Sam/Bam format ```

5.1 split split the sam,bam to chr_subFiles 5.2 msort msort the sam with -kn4 5.3 merge multi Sort sam,bam to a Sort Sam 5.4 rmdup remove PCR duplicates of SortSam,Bam 5.5 view view the AlignmentBam,Sam,Soap 5.6 stat stat Sort Sam,Bam of cov,depth... 5.7 filter fiter/extract the Sam,Bam Read 5.8 Alg2geno estimate genotype bases soap,bam,sam ```

Gfftools

6 Gfftools Tools for file of annotation gff format ```

6.1 getCdsPep Get CDS & Pep Seq based gffFile of genome 6.2 CDSSNP Get CDS SNP & synonymous or not 6.3 AnoSNP Annotation SNPs give Info ```

Formtools

7Formtools Tools for file format convert ```

7.1 Soap2Sam Soap -- Sam Format 7.2 Xam2Soap Bam,Sam -- Soap Format 7.3 Alg2Fq Soap,Bam,Sam -- Fq Format 7.4 CDS2Pep CDS seq -- Pep Format 7.5 Fq2Fa Fastq -- Fasta Format ```

Filetools

8 Filetools Tools for file with fixed format ```

8.1 split split FILE(s) to SubFile By Row-ID 8.2 msort sort all FILE(s) quick & low memory 8.3 merge merge multi Sort FILE(s) to a Sort FILE 8.4 SF Find Same or Diff in two Files 8.5 Fre stat Row Frequency Dis of FILE(s) 8.6 view view the AlignmentBam,Sam,Soap 8.7 AddRef Add the Ref base to the InPut files 8.8 less view the file like less 8.9 cat cat the file like cat & zcat ```

Gametools

9 Gametools package for some classics games ```

9.1 Snake Snake Greed Eat Game 9.2 DropRock Flee Drop Rock Game 9.3 LLK Lian Lian Kan Game 9.4 Puzzle Order digit in Puzzle 9.5 FindMine Mine sweep Game 9.6 Cal24 4 Num compute 24 Game 9.7 Sudoku Sudoku(SumNum) Game ```

summarize ```

Usage 7 1 Fatools introduce (Tools for file of FASTA format) 7 2 Fqtools introduce (Tools for file of FASTQ format) 9 3 SOAPtools introduce (Tools for file of mapping result SOAP format) 11 4 CNStools introduce (Tools for file of soapsnp result consensus) 14 5 Xamtools introduce (Tools for file of mapping result Sam/Bam format) 17 6 Gfftools introduce (Tools for file of annotation gff format) 19 7 Formtools introduce (Tools for file format convert) 20 8 Filetools introduce (Tools for file with fixed format) 21 9 Gametools introduce (package for some classics games) 23 Future 24 ```

```

Usage 1 Fatools introduce (Tools for file of FASTA format) This tools main include 12 foundation functions for dealing with FASTA format. Lists the following: 1.1 stat quick stat fasta's info 1.2 findN quick find fasta's N region 1.3 extract get fragments from seq based on coordinates 1.4 regenerate merge a new Ref Bases scaffolds 1.5 filter filter the short & too many 'N' Seq 1.6 cutF cut fasta to fixed Num of subFile in total 1.7 cutS cut fasta to fixed Num of Seq in each subfile 1.8 getSP get Seq by specified ID or pattern 1.9 getSN get Seq by specified order Num range 1.10 getCdsPep get CDS Seq & Pep Seq based the gffFile 1.11 CDS2Pep Translate CDS-Seq to protein-Seq 1.12 reform reform/modify the sequence 1.1 stat Quickly stat fasta file and give out each seq's info, consisting of length of N, effective length,length GC and the length of lower case acgt example: Usage:stat -InPut in.fa 1.2 findN Quickly give out the N-region for every sequence with small memory. Format : Chr start end example: Usage:findN -InPut in.fa 1.3 extract Main function is to extract some special regions sequence of sub-sequence. InPut region can also be a multi-Region file with format chr start end. User can also use parameters -Reverse,-Complemen to transform sub-sequence example: Usage:Extract -InPut in.fa -OutPut out.fa -ORegion chr:start:end -InPut str InPut fa for extract Sub Seq -OutPut str OutPut file -ORegion str only one Region,Formatchr:start:end -MRegion str multi Region file,Formatchr start end -Reverse reverse the sequence -Complement complement the sequence -help show this help 1.4 regenerate Main function is to merge the fragment of scaffolds to new long scaffolds virtual chromosome and give out their corresponding position relation. User can make a virtual genome with fixed length of newchr or the number of newchr. The program sort the scaffolds by length before merge, so the long scaffolds will be together. example: Usage: regenerate -InPut in.fa -OutPut out.fa 1.5 cutF This command function is to split the InPut fasta file to a fixed number of sub-files, default number of sub-files is 12. example: Usage:cutF -InFa in.fa 1.6 cutS This command function is to assign sub-sequence to a sub-file. default one sub-sequence is a sub-file. example: Usage: cutS -InFa in.fa If the default number of sub-sequence is 1, the sub-file will be named by itself seq-ID. User can split the genome to a chr-seq as example showing, 1.7 getSP Main function is to extract some pattern of sub-sequences. Parameters explain: -GetID : only get the sequences with the same with seq-ID -Pattern： get out seq that SeqID can match the specifed word. -UnPattern : get out seq that SeqID can’t match the specifed word. example: Usage:getSP -InFa in.cds.fa -Pattern 'AK' Help for detail -InFa str InPut Fa for get specifed Seq -GetID str get one sequence by specified ID -Pattern str get out Seq that can match the specifed word -UnPattern str get out Seq that can unmatch the specifed word -OutPut str OutPut Dir for cut FilesSTOUT -help show this help 1.8 getSN Main function is to extract an area of sub-sequences. example: Usage: getSN -InPut in.fa -Sample 5-10 As example show, the result will give the sequences from 5th-10th.we can get the fifth sequences using Parameters -Sample 5 1.9 filter 1) Filter the sequences that its length is too short. 2) Filter the sequences that 'N' length is too length. example: Usage:filter -InPut in.fa -OutPut out.fa 1.10 getCdsPep Main function is to get the CDS-Seq if the InPut fasta had its gene annotation files (gffFile). example: Usage:getCdsPep -Ref in.fa -Gff in.gff -OutPut out 1.11 CDS2Pep Translate the CDS-Sequences to the protein-Sequences. example: Usage:CDS2Pep -InCDS inCDS.fa -OutPut outPep.fa 1.12 reform Reform/modify the sequence. example: Usage:reform -InPut in.fa -Reverse -Complement -LowerCase

2 Fqtools introduce (Tools for file of FASTQ format) This tools main include 4 foundation functions for dealing with FASTQ format. Lists the following: 2.1 stat quick stat fastq's info 2.2 filter filter fastq for clean datas 2.3 rmAdapterPE index rm adapter data filter of PE 2.4 rmAdapterSE index rm adapter data filter of SE 2.5 pooling pooling index library data filter 2.1 stat Stat the Fq file to give out some information of it. Consisting of Number of Read,base , ratio of Q20,Q30... and the distribution of ACGTN along the read. example: Usage:stat -InFq 1.fq -InFq 2.fq -OutStat info.out 2.2 filter Filter and trim the low quality of Reads or Bases to get the clean Fqdata. Considering of large chunks of data, the OutPut will be compressed. 1)trim the bases that are continuous lowest quality at the end of the reads. 2) can filter the Reads that may is distributed wrong by index cut. 3) filter the Reads with too many 'N' 4) filter the Reads with too short 5) also standard output the statistics information of the fqdata example: Usage:filter -InFq1 A1.fq -InFq2 A2.fq -OutFq1 B1.fq -OutFq2 B2.fq options -InFq1 str file name of InFq1 InPut -InFq2 str file name of InFq2 InPut -OutFq1 str file name of OutFq1.gz OutPut -OutFq2 str file name of OutFq2.gz OutPut -MinBaseQ char the trim base quality B -MinLeng int the min Read length 30 -MaxLeng int the max Read length 100 -IndexCut cut off the index -OffN float the X of leng Read to cut0.5 -help show this help 2.3 rmAdapterPE Remove the Adapter of Reads in Pair-end Fqdata. example: Usage:rmAdapterPE 1.fq.gz2.fq.gz1.adapter.list.gz 2.adapter.list.gz outdir 2.3 rmAdapterSE Remove the Adapter of Reads in Single-end Fqdata. example: Usage:rmAdapterSE 1.fq.gz 1.adapter.list.gz outdir 2.4 pooling Distribute the Reads by sample where library is pooling by muti-sample example: Usage:pooling 1.fq.tr.gz 2.fq.tr.gz 1.adapter.list.gz 2.adapter.list.gz outdir sample_list_of_pooling index_id needrawdata 1:0

3 SOAPtools introduce (Tools for file of mapping result SOAP format) This tools main include 10 foundation functions for dealing with SOAP format. Lists the following: 3.1 split split soaplist by chr file 3.2 msort sort the SoapOut by chr and position 3.3 view view the Alignment of SoapBychrSort 3.4 merge merge multi SoapBychrSort to a Sort Soap 3.5 filter fiter/extract the soap Read 3.6 stat stat SortSoap of cov,depth,MisMacth... 3.7 rmdup remove PCR duplicates of SortSoap 3.8 genotype SortSoap--consistencygenotype,RST,Hit,Qseq... 3.9 Soap2Sam convert Soap 2 Sam Fomat 3.10 Xam2Soap convert Bam,Sam 2 Soap Fomat 3.1 split Split the SOAP result files to multi-Files by the mapping chromosome. One subFile (named by chr) is only the result that read mapped to this chromosome. At the same time give out the statistics information of the mapping result(insert size…) example: Usage:split -InFile 1.soap -InFile 2.soap -OutDir ODir -Ref Ref.fa -OutStat info.out As example show, it will OutPut a file that is the distribution of insert size, User can use the bin InsertDis2pdf.pl to draw the pdf. As bellow：

3.2 msort Sort the SOAP result by eighth and ninth row with more quickly and low memory. Comparing the linux sort , msort can read and write compressed files (gz). example: Usage:msort -k8 -kn9 In.soap -o In.soap Usage:msort -kn9 In.chrsoap.gz out.soap Usage:msort -k8 -kn9 In.soap -o Out.soap.gz 3.3 merge This command is to merge muti-SoapBychrSort-file which had been sorted to a big sorted SOAP File. The InPut soap must been sort and only have one chr result. It will work much better than linux cat | sort, and it will not occupation memory and run quickly. example: Usage:merge -InList soap.list -OutPut out.soap 3.4 filter Fiter the SOAP result or extract some SOAP result that fit some condition example: Usage:filter -InPut in.soap 3.5 view View the Alignment of SoapBychrSort in graphical representation. The InPut SOAP must be one chr and have been sort. And it similar to the samtools tview example: Usage:./iTools SOAPtools view -Ref ./chr38.fa -InPut ./chr38.sort.gz Then InPut "?" to see the help，also enter g（goto） to goto a special position . "T" to see quality ，"S" for alignment ， "R" for "Read-ID" , "D" for diff-base。 Such after Entering 'g' InPut =99384 or chr38:1009823 Enter "D" to see the base which is diff from the Ref base, As bellow: Enter "T" to see the quality of every base, As bellow: User can also enter the "?" to the more help: 3.6 stat For SOAP results that have been sorted. This will quickly and low memory to stat it and give out the information. Consisting of the mean depth,depth Dis,coverageand mismatch etc. User can also easy get depth of every sites only add parameter -sizeD example: Usage:stat -InFile 1.soap -OutStat info.out -Ref Ref.fa -SiteD int Out every sites Depth:0:NA;1:all_depth;2:uniq_depth 0 3.7 rmdup For SOAP result that have been sorted. This will quickly and low memory to remove PCR duplicates Reads example: Usage:rmdup -InPut in.sort.soap -OutPut out.soap 3.8 genotype Get the accuracy of consensus (genotype) from the SOAP result that have been sorted.At the same time, it will also give out the p-value of RST-test, mean-Hit(copynumber) and Qseq. example: Usage:Genotype -InPut In.soap -Ref Ref.fa -OutPut Out.geno 3.9 Soap2Sam & Xam2Soap Bam/Sam - - - - SOAP . See the Formtools for detail

4 CNStools introduce (Tools for file of soapsnp result consensus) This tools main is to deal with the result(cns & glf) of soapsnp(V1.02). Note:Glf fle is no the glf of soapsnpV1.06. And this tool main include 15 foundation functions. Lists the following: 4 CNStools Tools for file of soapsnp result consensus . Individual Usage: 4.1 ExtractCns Extract the potential snp from the cns file 4.2 FilterCns Filter the potential snp to get accurate SNP Population Usage: 4.3 GLFmulti Merge Glf(1.02) list to RawFile of Population 4.4 Addcn Add the copybernum for the RawFile 4.5 FilterRaw Filter Raw(+cp)Addcn file to get accurate Pop SNP 4.6 GLF2GPF Get the genotype from the glf List by Site 4.7 GLF2Geno Get the genotype from the glf List by Region 4.8 FilterGeno Filter genotype file to get accurate genotype SNP 4.9 MAF Stat Minor Allele Frequency in Raw or Addcn Tools Usage: 4.10 Fre Stat Row Frequency Distribution of file(List) 4.11 AddRef Add the Ref base to the InPut files 4.12 AddcnAll Add the copybernum for the RawFile 4.13 DepthGlf Stat the allele Depth distribution in glf(1.02) 4.14 DepthCns Stat the allele Depth Distribution in CNS 4.15 DepthRaw Stat allele Depth Distribution in Raw or Addcn Help Show this help

4.1 ExtractCns Extract the potential snp from the cns file example: Usage:ExtractCns -InPut in.cns -OutPut out.cns 4.2 FilterCns Filter the potential snp to get the accurate SNP example: Usage:FilterCns -InPut in.cns -OutPut out.cns -InPut str InPut the CNS file of potential SNP -OutPut str OutPut of accurate SNP -MinQual int the min qulity for snp20 -MaxCP float the max soap rep(copynumber) for snp2.0 -MinDist float the min distant for two snps1 -MinDepth float the min depth for two snps1 -MaxDepth float the max depth for two snps100 -help show this help 4.3 GLFmulti Main function is to integrate individual likelihood of genotypes (glf file) to produce a pseudo-genome for each site by maximum likelihood estimation. And it give out some stat information ,such depth dis of every sample. example: Usage:GLFmulti -GlfList in.glflist -OutPut out.raw 4.4 Addcn Get every site’s mean-hit number (copynumber : Average copy number of nearby this site) quickly and low memory form SOAP result . Here OutPut file suffix is add_cn. example: Usage:Addcn -InRaw in.raw -SoapList SoapBychr.list -OutPut out.addcn 4.5 FilterRaw Filter the file with copynumber suffix is addcn to get the accurate Pop SNP example: Usage:FilterRaw -InAddcn in.addcn -OutPut out.addcn options 4.6 GLF2GPF Get every sample’s genotype from glf file list at given position ,also user can add parameter to get the depth information. example: Usage:GLF2GPF -Indbsnp in.dbdnp -GlfList in.glflist -OutPut out.genotype 4.7 GLF2Geno Get every sample’s genotype from glf file list at given regions, user can also add parameter to get the depth information. Example: Usage:GLF2Geno -GlfList in.glflist -OutPut out.genotype -GlfList str Glf List file InPut -OutPut str file name of OutPut genotype -Start int the Start position to Run0 -End int the End position to Runchr_end -DepthOUT Print the infomation of DepthNA -help show this help 4.8 FilterGeno Fiter the site that population genotype is can’t fit condition. 1) Filter the site that all samples are the same allele. 2) Filter the site that too much sample missing data at this sites 3) Choice to filter or not the sie that have three alleles. 4) Choice to filter or not the sie that have many heterozygosis genotype. example: Usage:FilterGeno -InPut in.genotype -OutPut out.genotype 4.9 AddRef Add the ref allele at the given position quickly and low memory. InPut file first row is chr name .second row is position. example Usage:AddRef -InPut inFile -Ref in.fa -OutPut out 4.10 AddcnAll Get every site’s mean-hit number (copynumber : Average copy number of nearby this site) quickly and low memory form SOAP/Sam/Bam result . Here OutPut file suffix is add_cn. Bam/Sam read will be unique mapping if carrying no this information. example: Usage:AddcnAll -InRaw in.raw -SoapList SoapBychr.list -OutPut out.addcn 4.11 Fre Main function is to stat the distribution of appointed row in File(s) .Such like depth dis,etc. example: Usage:Fre -InFile inFile -OutPut out -Row 4 -Bin 0.1 4.12 DepthGlf Get the Depth distribution from the glf file. And it also can give out every site’s depth in fa format. example: Usage:DepthGlf -InPut in.glf -OutPut out.depth 4.13 DepthCns & DepthRaw Stat the depth distribution of cns file and raw file. It the special case of CNStools Fre Fre Bin=1,Row=14 or 4. example: Usage:DepthCns -InPut in.cns -OutPut out.depth DepthRaw -InPut in.raw -OutPut out.depth 4.14 MAF Stat the minor allele frequency distribution of SNP file format raw/addcn. example: Usage:MAF -InFile in.raw -OutPut out.maf Usage:MAF -InListin.addcn.list -OutPut out.maf

5 Xamtools introduce (Tools for file of mapping result Sam/Bam format) This tools main include 10 foundation functions for dealing with Sam/Bam format. Lists the following: 5 Xamtools Tools for file of mapping result Sam/Bam format 5.1 split split the sam,bam to chr_subFiles 5.2 msort msort the sam with -kn4 5.3 merge multi Sort sam,bam to a Sort Sam 5.4 rmdup remove PCR duplicates of SortSam,Bam 5.5 view view the AlignmentBam,Sam,Soap 5.6 stat stat Sort Sam,Bam of cov,depth... 5.7 filter fiter/extract the Sam,Bam Read 5.8 Alg2geno estimate genotype bases soap,bam,sam 5.1 split Split the Sam/Bam result files to multi-Files by the mapping chromosome. One subFile (named by chr) is only the result that read mapped to this chromosome. Parameter -SamNoHead is for sam file with no head. example: Usage: split -Ref Ref.fa -InFile in1.sam -InFile in2.sam 5.2 msort Apply msort to sort the sam file . example: Usage:msort -kn4 A.sam.gz -o B.sam.gz 5.3 merge This command is to merge muti-Sam/Bam which had been sorted to a big sorted Sam.gz File. The InPut soap must been sort and only have one chr result. It will work much better than linux cat | sort, and it will not occupation memory and run quickly. example: Usage:merge -InList sam.list -OutPut out.sam -SamNoHead 5.4 rmdup For Sam/Bam result that have been sorted. This will quickly and low memory to remove PCR duplicates Reads example: Usage:rmdup -InBam in.sort.bam -OutPut out.sam 5.4 view View the Alignment of Sam/Bam in graphical representation. The InPut Sam/Bam must be one chr and have been sort. And it similar to the samtools tview. Detailed usage see the SOAPtools view. 5.5 stat For Sam/Bam results that have been sorted. This will quickly and low memory to stat it and give out the information. Consisting of the mean depth,depth Dis,coverageand mismatch etc. User can also easy get depth of every sites only add parameter -sizeD example: Usage: stat -InFile 1.sam -OutStat info.out -Ref Ref.fa -SiteD int Out every sites Depth:0:NA;1:all_depth;2:uniq_depth 0 5.6 Filter Fiter the Sam/Bam result or extract some Sam/Bam result that fit some condition example: Usage:filter -InPut in.sam 5.7 Alg2geno Get the accuracy of consensus (genotype) from the alignment result that have been sorted. At the same time, it will also give out the p-value of RST-test, mean-Hit(copynumber) and Qseq. Similar to SOAPtools genotype. 5.8 Xam2Soap Sam,Bam/Soap format, See the Formtools in detail

6 Gfftools introduce Tools for file of annotation gff format This tools main include 3 foundation functions for dealing with Gff format. Lists the following: 6 Gfftools Tools for file of annotation gff format 6.1 getCdsPep Get CDS & Pep Seq based gffFile of genome 6.2 CDSSNP Get CDS SNP & synonymous or not 6.3 AnoSNP Annotation SNPs give Info

6.1 getCdsPep Same to the Fatools getCdsPep. Pls see there for help. 6.2 CDSSNP Get the SNP in CDS region and judge it is synonymous or not Example: Usage:CDSSNP -Ref in.fa -Gff in.gff -SNP in.raw 6.3 AnoSNP Base the genome gene annotation gff file to annotate SNPs are in which region.UTR,CDS,intron,ect. example: Usage:AnoSNP -Gff in.gff -SNP in.snp -OutPut out.snp.info

7 Formtools introduce (Tools for file format convert) This tools main include 5 foundation functions for converting file format. Lists the following: 7.1 Soap2Sam Soap -- Sam Format 7.2 Xam2Soap Bam,Sam -- Soap Format 7.3 Alg2Fq Soap,Bam,Sam -- Fq Format 7.4 CDS2Pep CDS seq -- Pep Format 7.5 Fq2Fa Fastq -- Fasta Format

7.1 Soap2Sam Convert Soap Format to Sam format，improvement the Soap2Sam.pl which is writed lh3. User can add parameter -NoOri if the pair-end read are no together in the soap format. (also can read gz) example: Usage:Soap2Sam -InSoap in.soap -OutSam out.sam -InSoap str InPut SortSoap file -OutSam str OutPut Sam file -Pair if soap is PairOut,for flag -NoOri if soap is no original same ReadID No Neighbors -Dict str InPut Sam Head file -help show this help 7.2 Xam2Soap Convert sam /bam format file to Soap format file. example: Usage: Xam2Soap -InBam in.bam -OutPut Out.soap 7.3Alg2Fq Convert sam/bam and soap back to fq format，also specified deal with read that map to minus strand example Usage:Alg2Fq -InBam in.bam -OutPut Out.fq 7.4 CDS2Pep Translate the CDS-Sequences to the protein-Sequences. example: Usage:CDS2Pep -InCDS inCDS.fa -OutPut outPep.fa 7.5 Fq2Fa Translate Fastq format file to the Fasta format file. example: Usage:Fq2Fa -InFq in.fq -OutPut out.fa

8 Filetools introduce (Tools for file with fixed format) This tools main include 9 foundation functions for specified file format. Lists the following: 8.1 split split FILE(s) to SubFile By Row-ID 8.2 msort sort all FILE(s) quick & low memory 8.3 merge merge multi Sort FILE(s) to a Sort FILE 8.4 SF Find Same or Diff in two Files 8.5 Fre stat Row Frequency Dis of FILE(s) 8.6 view view the AlignmentBam,Sam,Soap 8.7 AddRef Add the Ref base to the InPut files 8.8 less view the file like less 8.9 cat cat the file like cat & zcat

8.1 split Split FILE(s) to sub-File by the given row-ID. example: Usage: split -ChrList Ref.fa.chrlist -InList sam.list -Row 3 8.2 msort Sort File like linux sort, which can read the compressed File (#.gz) and can also write compressed File (#.gz) 8.3 merge This command is to merge muti-files which had been sorted to a big sorted compressed File by specified row-ID example: Usage: merge -InList sam.list -OutPut out.sam -Row 4 8.4 SF through comparing some Row of two File, give out all kind of the collection of these two files. example: Usage: SF -InFile1 A.in -InFile2 B.in -ID1 1,2 -ID2 4,3 -InFile1 str InPut File1 for same or diff -InFile2 str InPut File2 for same or diff

-ID1 int The ID in the File1 row 1,2 2 -ID2 int The ID in the File2 row 1,2 2 -OutPut str OutPut File, or STDOUT -Swich int 1: same in file2 ;2 : diff in file1 ; 1 3: diff in file2 ;4 : same in file1 ; 1 6: same in file1 & file2 -help show this help

8.5 Fre Main function is to stat the distribution of appointed row in File(s) .Such like depth dis,etc. Similar to CNStools Fre, please seeCNStools Fre for detailed help example: Usage:Fre -InFileinFile -OutPut out -Row 4 -bin 0.1 8.6 Alg2geno Similar to CNStools Alg2geno, please see there for detailed help example: Usage:Alg2geno -InSoap In.soap -Ref Ref.fa -OutPut Out.geno 8.7 view Similar to XamTools view, please see there for detailed help example: Usage: view -InBam in.bam -Ref Ref.fa 8.8 less Similar to Linux less, see the tex files. '?' for help. '/' for com-model example: Usage: less file.txt 8.8 cat Similar to Linux cat &zcat, example: Usage: cat chr*.raw All.raw

9. Gametools introduce ( package for some classics games) A package for some classics games. Snake Snake Greed Eat Game DropRock Flee Drop Rock Game LLK Lian Lian Kan Game Puzzle Order digit in Puzzle FindMine Mine sweep Game Cal24 4 Num compute 24 Game Sudoku Sudoku(SumNum) Game

Help Show this help

Intelligence Game: 9.1 ./iTools Gametools Sudoku Sudoku game . All number of every direction sum to the same number. And every number only appears once. User can enter "K" to see answer. Sustaining mouse handle . 9.2 ./iTools Gametools Puzzle A game like puzzle .Let the Number from small to large in the table.From left to right ,from up to down. Sustaining mouse handle . 9.3 ./iTools Gametools Cal24 Four of playing cards ,Use arithmetic(+-*/) and bracket to let the value is 24. 9.4 ./iTools Gametools FindMine Like window to sweep the Mine . Sustaining mouse handle .

Relaxation game 9.5 ./iTools Gametools LLK Lian lian Kan game, "f" for fast,"l" for slow. 9.6 ./iTools Gametools Snake Eating Snake game 9.7 ./iTools Gametools DropRock Flee Drop Rock in space game.

Future Our overall goal is to provide an abundant toolkit for next-generation DNA Re-Sequencing analysis, the researchers can get all kinds of normal analyses application in this toolkit, and we will also enrich and update the toolkit according to the new requirements. Furthermore, we also provide and develop some scalable analysis pipelines based this toolkit. Bioinformatics analyst can easy and quickly analyze Re-Sequencing data. We can get SNP genotype data from raw fqdata just through the pipeline above. Finally, this toolkit framework is available through a distributed source code repository, which makes it easy for developers to create derivative module and application, through discussion about this toolkit, we hope the researchers can promote communication of their biological research and together maintain this toolkit.

Thanks to all.

Swimming in the sky and flying in the sea hewm@genomics.org.cn 2012-05-20

Program: iTools Version: 0.16 hewm@genomics.org.cn May 25 2012 Usage:

Fatools Tools For Fasta Fqtools Tools For Fastq SOAPtools Tools For SOAP CNStools Tools For CNS Xamtools Tools For Sam/Bam Gfftools Tools For Gff Formtools Tools For Form convert Filetools Tools For File Othertools Tools For Other Gametools Tools For Game

Help Show help in detail

FaTools Usage:

stat quick stat fasta's info findN quick find fasta's N region extract get fragments from seq based on coordinates regenerate merge a new Ref Bases scaffolds filter filter the short & too many 'N' Seq cutF cut fasta to fixed Num of subFile in total cutS cut fasta to fixed Num of Seq in each subfile getSP get Seq by specified ID or pattern getSN get Seq by specified order Num range getCdsPep get CDS Seq & Pep Seq based the gffFile CDS2Pep Translate CDS-Seq to protein-Seq reform reform/modify the sequence

Help Show this help

Usage: stat -InPut in.fa

-InPut str Input fa for stat the length

-OutPut str Output file,otherwiseSTDOUT

-help show this help

Usage: findN -InPut in.fa

-InPut str InPut fa for find N Region

-OutPut str OutPut file,otherwiseSTDOUT

-help show this help

Usage: extract -InPut in.fa -OutPut out.fa -ORegion chr:start:end

-InPut str InPut fa for extract Sub Seq -OutPut str OutPut file -ORegion str only one Region,Formatchr:start:end -MRegion str multi Region file,Formatchr start end

-Reverse reverse the sequence -Complement complement the sequence

-help show this help

Usage: regenerate -InPut in.fa -OutPut out.fa

-InPut str Input fa for regenerate -OutPut str Output file fa of new Ref

-oriChr str Original chr name for NoChangChr -newChr str New Chr for merge SeqNewChr -insertN int Insert Num of N between two Scaf 100 -numSeq int the Num for merge new Seq 20 -length int Len of each new merge Seq NA

-help show this help

Usage: filter -InPut in.fa -OutPut out.fa

-InPut str Input fa for filter -OutPut str Output file

-MinLen int The MinLength for Seq to pass1000 -NRatio float The max ratio of miss N Length0.5

-help show this help

Usage: cutF -InFa in.fa

-InFa str Input Fa for cut to subFile

-OutDir str Output Dir for cut Files PWD -Cut int Num of subFile for cut Fa 12

-help show this help

Usage: cutS -InFa in.fa

-InFa str Input Fa for cut to subFile

-OutDir str Output Dir for cut Files PWD -Cut int Num of seq for each subFile 1

-help show this help

Usage: getSP -InFa in.cds.fa -Pattern 'AK'

-InFa str Input Fa for get specifed Seq -GetID str get one sequence by specified ID -Pattern str get out Seq that can match the specifed word -UnPattern str get out Seq that can unmatch the specifed word

-OutPut str Output Dir for cut FilesSTOUT -help show this help

Usage: getSN -InPut in.fa -Sample 5-10

-InPut str Input fa for geting Sub range Seq -Sample str get Seq by specified order range Only give one num will only extract one Seq

-OutPut str Output file STOUT

-help show this help

Usage: getCdsPep -Ref in.fa -Gff in.gff -OutPut out

-Ref str Input Ref fa -Gff str Input Ref gff -OutPut str Output cds seq file

-help show this help

Usage: CDS2Pep -InCDS inCDS.fa -OutPut outPep.fa

-InCDS str Input CDS fa -OutPut str Output pep file

-Warning cerrOut the wrong CDS SeqID -help show this help

Usage: reform -InPut in.fa

-InPut str Input fa for upper/lower case

-OutPut str OutPut file STOUT -LowerCase Lower the fa baseUpperNA -Reverse reverse the sequence -Complement complement the sequence

-help show this help

FqTools Usage:

stat quick stat fastq's info filter filter fastq for clean datas rmAdapterPE index remove adapter of PE rmAdapterSE index remove adapter of SE pooling pooling index library data filter

Help Show this help zhanghaikuan@genomics.cn

Usage: stat -InFq 1.fq -InFq 2.fq -OutStat info.out

-InFq str Repeat Input Fq File for stat -InFqList str Input Fq File List for stat -OutStat str Out file of stat

-MinBaseQ char Min base quality @ -CPU int Number of Thread 1

-help show this help

Usage:filter -InFq1 A1.fq -InFq2 A2.fq -OutFq1 B1.fq -OutFq2 B2.fq options

-InFq1 str file name of InFq1 Input -InFq2 str file name of InFq2 Input -OutFq1 str file name of OutFq1.gz output -OutFq2 str file name of OutFq2.gz output

-MinBaseQ char the trim base quality B -MinLeng int the min Read length 30 -MaxLeng int the max Read length 100 -IndexCut cut off the index -OffN float cut N reach X% of read length0.5 -help show this help

Usage: rmAdapterPE 1.fq.gz 2.fq.gz 1.adapter.list.gz 2.adapter.list.gz outdir

Usage: rmAdapterSE 1.fq.gz 1.adapter.list.gz outdir

Usage: pooling 1.fq.tr.gz 2.fq.tr.gz 1.adapter.list.gz 2.adapter.list.gz outdir sample_list_of_pooling needrawdata 1:0

Program: SOAPtools (Tools for Soap output) Version: 0.21 hewm@genomics.org.cn 2012-02-24

SOAP Usage:

split split soaplist by chr file msort sort the SoapOut by chr and position view view the Soap Alignment merge merge multi SoapBychrSort to a Sort Soap filter fiter/extract the soap Read stat stat SortSoap of cov,depth,MisMacth... rmdup remove PCR duplicates of SortSoap genotype SortSoap--consistencygenotype,RST,Hit,Qseq...

Soap2Sam Soap -- Sam Fomat Xam2Soap Bam,Sam -- Soap Fomat

Help Show this help

Usage: split -InFile 1.soap -InFile 2.soap -OutDir ODir -Ref Ref.fa -OutStat info.out

-InFile str Repeat Input soap file for split -InList str Input soap file List for split -Ref str InPut Ref seq -OutStat str Out file of stat the Insert size

-OutDir str Output Dir for split file./ -NoOutgz OutPut file with No gz NA

-help show this help

msort -k8 -kn9 In.soap -o In.soap Example: msort -kn9 In.chrsoap.gz out.soap msort -k8 -kn9 In.soap -o Out.soap.gz

Usage: msort -hrfn -t filed_separators -k rfmnecolstart-end{enum1,...},... file Options: -h display this document -l specify line brokers, you can define more than one characters defaultly, they are newline -L treat N line as a block, defaultly N = 1 -t specify field separators, you can define more than one characters defaultly, they are space, tab -r reverse sort, it will be overwritten if fileds are specified -f ignore character`s case, ... -n treat fileds as number, ... -m treat fileds as number or string, ... -o OutPut the files#.gz or not,Otherwise to STDOUT -k specify fileds to be sorted, eg. rn102-6: reverse sort 2-6 (include 6) of column 10, treat it as number n11: sort column 11, treat it as number f26-: sort 6-end of column 2, treat it as string, ignore case rfm3: reverse sort column 3, treat it as string or number, ignore string case f3{red green blue}: sort column 3 , treat it as enum, ignore string case If given filefile.gz,read info from file, otherwise from STDIN

Usage: view -InPut in.soap -Ref Ref.fa

-InPut str Input SortSoapByChr

-Ref str Input Ref Seq fa -MinBaseQ char The min Seq Quality '@'

-help show this help

Usage: merge -InList soap.list -OutPut out.soap

-InList str Input SoapBychrSortgz file List for merge -OutPut str Output file of merge sort soap

-OutNogz OutPut file with NO gz

-help show this help

Usage: filter -InPut in.soap

-InPut str InPut Soap File

-OutPut str OutPut file/file.gz,or STDOUT -MaxHit int the max hit of read1 -MinLeng int the min length of read30 -Start int the start position out0 -End int the end position out1e10 -Chr str only the chr outall

-help show this help

Usage: stat -InFile 1.soap -OutStat info.out -Ref Ref.fa

-InFile str Input SortSoap file for Stat -InList str Input SortSoapByChr file List for Stat -Ref str Input Ref seq -OutStat str Out file of stat

-SiteD int Out every sites Depth0 0,1,20:NA;1:all_depth;2:uniq_depth -help show this help

Usage: rmdup -InPut in.sort.soap -OutPut out.soap

-InPut str Input SortSoap file -OutPut str Output file with rmdup

-IDFlag int Add Flag to ReadID for SoapSVNA -help show this help

Usage: genotype -InPut In.soap -Ref Ref.fa -OutPut Out.geno

-InPut str InPut SortSoap file for Genotype -Ref str InPut Ref seq -OutPut str OutPut genotype file

-MinBaseQ char The minimum Seq base quality '@' -HET float Novel HET prior probability 0.0010 -Haploid If the specie is haploid or chrY diploid

-help show this help

Program: CNStools (Tools for SoapSNP output) Version: 0.10 hewm@genomics.org.cn 2011-12-12 Individual Usage:

ExtractCns Extract the potential snp from the cns file FilterCns Filter the potential snp to get accurate SNP

Population Usage:

GLFmulti Merge Glf(1.02) list to RawFile of Population Addcn Add the copybernum for the RawFile FilterRaw Filter Raw(+cp)Addcn file to get accurate Pop SNP GLF2GPF Get the genotype from the glf List by Site GLF2Geno Get the genotype from the glf List by Region FilterGeno Filter genotype file to get accurate genotype SNP MAF Stat Minor Allele Frequency in Raw or Addcn

Tools Usage:

Fre Stat Row Frequency Distribution of file(List) AddRef Add the Ref base to the input files AddcnAll Add the copybernum for the RawFile DepthGlf Stat the allele Depth distribution in glf(1.02) DepthCns Stat the allele Depth Distribution in CNS DepthRaw Stat allele Depth Distribution in Raw or Addcn

Help Show this help

Usage: ExtractCns -InPut in.cns -OutPut out.cns

-InPut str Input the CNS file -OutPut str Output of the Potential snp

-help show this help

Usage: FilterCns -InPut in.cns -OutPut out.cns

-InPut str InPut the CNS file of potential SNP -OutPut str OutPut of accurate SNP

-MinQual int the min qulity for snp20 -MaxCP float the max soap rep(copynumber) for snp2.0 -MinDist float the min distant for two snps1 -MinDepth float the min depth for two snps1 -MaxDepth float the max depth for two snps100

-help show this help

Usage: GLFmulti -GlfList in.glflist -OutPut out.raw

-GlfList str glf file input list -OutPut str file name of output raw

-Start int the start position to run1 -End int the end position to runchrEnd -help show this help

Usage: Addcn -InRaw in.raw -SoapList SoapBychr.list -OutPut out.addcn

-InRaw str Input file of GLFmulti raw -SoapList str soap by chr list -OutPut str OutPut addcn file with copyberNum -ChrLeng int The length of the chr ref

-CPU int Number of thread for Run 2 -help show this help

Usage:FilterRaw -InAddcn in.addcn -OutPut out.addcn options -InAddcn str file name of input addcn file -OutPut str file name of output

-MinDepth int the filter of the lowest depth 68 -MaxDepth int the filter of the hightest depth 1168 -Quality double the filter of the snp quility 15 -CpNumber float the filter of the copynumber 1.5 -Name str the name of the speci for dbsnp HG

-help show this help

Usage: GLF2GPF -Indbsnp in.dbdnp -GlfList in.glflist -OutPut out.genotype -Indbsnp str file name of input sort dbsnp file -GlfList str Glf List file input -OutPut str file name of output genotype

-DepthOUT Print the infomation of DepthNA

-help show this help

Usage: GLF2Geno -GlfList in.glflist -OutPut out.genotype -GlfList str Glf List file InPut -OutPut str file name of OutPut genotype

-Start int the Start position to Run0 -End int the End position to Runchr_end -DepthOUT Print the infomation of DepthNA

-help show this help

Usage: FilterGeno -InPut in.genotype -OutPut out.genotype

-InPut str InPut file of genotype -OutPut str OutPut the filter file

-Het float the max ratio of het allele0.88 -Miss float the max ratio of miss allele0.88 -Cut3base Filter position with 3 alleleoff -help show this help

Usage: MAF -InFile in.raw -OutPut out.maf

-InFile str Input raw or the addcn file -InList str Input raw or the addcn list file -OutPut str OutPut Minor Allele Frequency file

-help show this help

Usage: AddRef -InPut inFile -Ref in.fa -OutPut out

-InPut str Input file by chr(chr posi ...) -Ref str Input Chr Ref fastat file -OutPut str Output of the file with ref_base

-help show this help

Usage: AddcnAll -InRaw in.raw -SoapList SoapBychr.list -OutPut out.addcn

-InRaw str Input file of GLFmulti raw -SoapList str soap by chr list -BamList str bam by chr list -Sam:ist str sam by chr list -OutPut str output addcn file with copyNumber -ChrLeng int The length of the chr ref

-AllSite output copyNumber for all siteNA

-help show this help

Usage: DepthGlf -InPut in.glf -OutPut out.depth

-InPut str InPut the glf file -OutPut str OutPut of the depth dis

-AllSite Print every Site depthNA

-help show this help

Usage: DepthCns -InPut in.cns -OutPut out.depth

-InPut str Input cns file -OutPut str Output of the depth dis

-help show this help

Usage: DepthRaw -InPut in.raw -OutPut out.depth

-InPut str InPut raw or the addcn file -OutPut str OutPut of the depth4 row dis

-help show this help

Xamtools Usage:

split split the sam,bam to chr_subFiles msort msort the sam with -kn4 merge multi Sort sam,bam to a Sort Sam rmdup remove PCR duplicates of SortSam,Bam view view the AlignmentBam,Sam,Soap stat stat Sort Sam,Bam of cov,depth... filter fiter/extract the Sam,Bam Read Alg2geno estimate genotype bases soap,bam,sam

Xam2Soap Sam,bam Format to Soap Format Help Show this help

Usage: split -Ref Ref.fa -InFile in1.sam -InFile in2.sam

-Ref str Input the Ref seq -InFile str Repeat Input sam,bam file -InList str Input sam,bam file list

-OutDir str Output Dir for split sam ./ -Bam if the file is Bam format -SamNoHead if the file is Sam with NoHead -help show this help

Usage:msort -kn4 A.sam.gz -o B.sam.gz

Usage: merge -InList sam.list -OutPut out.sam

-InList str Input sort sam,bam file list -OutPut str Output Sort file for merge sam

-Bam if the file is Bam format -SamNoHead if the file is Sam with NoHead -help show this help

Usage: rmdup -InBam in.sort.bam -output out.sam

-InBam str Input SortBam file -InSam str Input SortBam file -OutPut str Output Sam file with rmdup

-IDFlag int Add Flag to ReadID -SamNoHead if the file is Sam with NoHead -help show this help

Usage: view -InBam in.bam -Ref Ref.fa

-InBam str Input SortBamByChr -InSam str Input SortSamByChr -InSoap str Input SortSoapByChr

-Ref str Input Ref Seq fa -MinBaseQ char The min Seq Quality '@' -SamNoHead if the file is Sam with NoHead

-help show this help

Usage: stat -InFile 1.sam -OutStat info.out -Ref Ref.fa

-InFile str Input Sort Sam,Bam file for Stat -InList str Input Sort Sam,Bam ByChr file List for Stat -Ref str Input Ref seq -OutStat str Out file of stat

-Bam If InPut File is Bam -SiteD int Out every sites Depth0 0,1,20:NA;1:all_depth;2:uniq_depth -help show this help

Usage: filter -InBam in.bam

-InSam str InPut Sam File -InBam str InPut Bam File

-OutPut str OutPut file/file.gz,or STDOUT -MinMapQ int The min Bwa Mapping Q 15 -MaxHit int The max Bwa Mapping Hit1 -MinLeng int the min length of read30 -Start int the start position out0 -End int the end position out1e10 -Chr str only the chr outall -SamNoHead if the file is Sam with NoHead

-help show this help

Usage: Alg2geno -InSoap In.soap -Ref Ref.fa -OutPut Out.geno

-InSoap str Input SortSoap file for Genotype -InBam str Input SortBam for Genotype -InSam str Input SortSam for Genotype -Ref str Input Ref seq -OutPut str Out Put genotype file

-MinMapQ int The minimum Bwa Mapping quality 15 -NOFiGap No Filter Bwa Del or Inset(Gap) Reads NA -BaseFilter int The minimum Base quality to pass 15 -MinBaseQ char The minimum Seq base quality '@' -HET float Novel HET prior probability 0.0010 -Haploid If the specie is haploid or chrX diploid

-help show this help

Gff Tools Usage:

getCdsPep Get CDS & Pep Seq based gffFile of genome CDSSNP Get CDS SNP & synonymous or not AnoSNP Annotation SNPs give Info

Help Show this help

Usage: getCdsPep -Ref in.fa -Gff in.gff -OutPut out

-Ref str Input Ref fa -Gff str Input Ref gff -OutPut str Output cds seq file

-help show this help

Usage: CDSSNP -Ref in.fa -Gff in.gff -SNP in.raw

-Ref str Input Ref fa -Gff str Input Ref gff -SNP str Input SNP File contact Format

-OutDir str Output Dir Path ./ -Format str SNP Input Form (cns/raw/add_ref)raw -MAllele Use main Allele as AncestorBase ref -help show this help

Usage: AnoSNP -Gff in.gff -SNP in.snp -OutPut out.snp.info

-SNP str Input SNP File Format (chr pos) -Gff str Input Ref gff -OutPut str Input after annotation SNP

-PrintNA print All SNP pos intergenic -help show this help

Form Tools Usage:

Soap2Sam Soap -- Sam Format Xam2Soap Bam/Sam -- Soap Format Alg2Fq Soap/Bam/Sam -- Fq Format CDS2Pep CDS seq -- Pep Format Fq2Fa Fastq -- Fasta Format

Help Show this help

Usage: Soap2Sam -InSoap in.soap -OutSam out.sam

-InSoap str Input SortSoap file -OutSam str Output Sam file

-Pair if soap is PairOut,for flag -Dict str Input Sam Head file -NoOri if soap is no original same ReadID No Neighbors

-help show this help

Usage: Xam2Soap -InBam in.bam -OutPut Out.soap

-InSam str Input Sam Format file -InBam str Input Bam Format file -OutPut str OutPut the SoapFormat file

-help show this help

Usage: Alg2Fq -InBam in.bam -OutPut Out.fq

-InSoap str Input Soap Format file -InSam str Input Sam Format file -InBam str Input Bam Format file -OutPut str OutPut the Fq Format file

-UnMap only output UnMapp read NA -help show this help

Usage: CDS2Pep -InCDS inCDS.fa -OutPut outPep.fa

-InCDS str Input CDS fa -OutPut str Output pep file

-Warning cerrOut the wrong CDS SeqID -help show this help

Usage: Fq2Fa -InFq in.fq -OutPut out.fa

-InFq str Input Fastq File -OutPut str Output Fasta file

-help show this help

File Tools Usage:

split split FILE(s) to SubFile By Row-ID msort sort all FILE(s) quick & low memory merge merge multi Sort FILE(s) to a Sort FILE SF Find Same or Diff in two Files Fre stat Row Frequency Dis of FILE(s) view view the AlignmentBam,Sam,Soap AddRef Add the Ref base to the input files less view the file like less cat cat the file like cat & zcat

Help Show this help

Usage: split -ChrList Ref.fa.chrlist -InList soap.list

-ChrList str Input the chrList -InFile str Repeat Input sam,bam file -InList str Input sam,bam file list

-OutDir str Output Dir for split SubFile./ -Row int the row Num of the chr name8 -help show this help

Usage: merge -InList sam.list -OutPut out.sam -Row 4

-InList str Input sort SubFile list -OutPut str Output Sort file for merge

-Row int the row Number of the sort9 -help show this help

Usage: SF -InFile1 A.in -InFile2 B.in

-InFile1 str Input File1 for same or diff -InFile2 str Input File2 for same or diff

-ID1 int The ID in the File1 row 1,2 2 -ID2 int The ID in the File2 row 1,2 2 -OutPut str OutPut File, or STDOUT -Swich int 1: same in file2 ;2 : diff in file1 ; 1 3: diff in file2 ;4 : same in file1 ; 1 6: same in file1 & file2 -help show this help

Usage: Fre -InFile inFile -OutPut out options

-InFile str : Input file for stat -InList str : Input file list for stat -OutPut str : OutPut file

-Row int : The row to count frequency 4 -Bin float : Window bin of frequency 1

-help : Show this help

Usage: view -InBam in.bam -Ref Ref.fa

-InBam str Input SortBamByChr -InSam str Input SortSamByChr -InSoap str Input SortSoapByChr

-Ref str Input Ref Seq fa -MinBaseQ char The min Seq Quality '@' -SamNoHead if the file is Sam with NoHead

-help show this help

Usage: less file.txt

Usage: cat *.raw

-InFile str Input file for Cat -InList str Input file List for Cat

-OutPut str Out file of Cat STDOUT

-help show this help

GameTools Usage:

Snake Snake Greed Eat Game DropRock Flee Drop Rock Game LLK Lian Lian Kan Game Puzzle Order digit in Puzzle FindMine Mine sweep Game Cal24 4 Num compute 24 Game Sudoku Sudoku(SumNum) Game

Help Show this help ```