PageName ▼	Summary + Labels ▼	Changed ▼	ChangedBy ▼	...
	BGB_delete_track	Delete a Biopieces Genome Browser track.	Dec 2009	martinah...@gmail.com
	BGB_intersect	Intersects two tracks in the Biopieces Genome Browser.	Dec 2009	martinah...@gmail.com
	BGB_list	List Biopieces Genome Browser tracks.	Dec 2009	martinah...@gmail.com
	BGB_read_track	Read Biopieces Genome Browser track into the stream.	Dec 2009	martinah...@gmail.com
	BGB_upload	Upload data to a local Biopieces Genome Browser.	Mar 2010	martinah...@gmail.com
	BiopiecesGenomeBrowser	Biopieces Genome Browser - a light weight genome browser	Mar 2010	martinah...@gmail.com
	FAQ	Featured	Feb 29	martinah...@gmail.com
	HowTo	A collection of Howtos   Featured	Apr 4	martinah...@gmail.com
	Installation	Installation intructions for Biopieces   Featured	Dec 14	martinah...@gmail.com
	Introduction	Introduction to Biopieces   Featured	Dec 14	martinah...@gmail.com
	KissFormat	The KISS format - a simple text based data format in 12 tab-separated columns	Jan 2011	martinah...@gmail.com
	PublicationsUsingBiopieces	List of publications using Biopieces.	May 11	martinah...@gmail.com
	add_ident	Add a unique identifier to each record in the stream.	May 2011	martinah...@gmail.com
	align_pair_seq	Pairwise align sequences from the stream.	Jun 2009	martinah...@gmail.com
	align_seq	Align sequences in the stream.	Aug 2010	martinah...@gmail.com
	analyze_assembly	Analyze assembled sequences in the stream and output stats.	May 2011	martinah...@gmail.com
	analyze_bed	Analyze BED entries in the stream.	May 2009	martinah...@gmail.com
	analyze_gc	Analyzes the GC composition of sequences in the stream.	Aug 2010	martinah...@gmail.com
	analyze_seq	Analyzes the sequence composition of sequences in the stream.	Oct 2010	martinah...@gmail.com
	analyze_snp	Analyzes mismatches and indels from ALIGN descriptors in the stream.	Nov 2009	martinah...@gmail.com
	analyze_tags	Analyze sequence tags in sequence or BED records from the stream.	May 2009	martinah...@gmail.com
	analyze_vals	Determine type, count, min, max, sum and mean for values in stream.	Aug 2010	martinah...@gmail.com
	assemble_contigs	Assemble contigs from mapping results in the stream.	Apr 2011	martinah...@gmail.com
	assemble_seq_idba	Assemble sequences in the stream using IDBA.	Dec 14	martinah...@gmail.com
	assemble_seq_ray	Assemble sequences in the stream using Ray.	Dec 14	martinah...@gmail.com
	assemble_seq_velvet	Assemble sequences in the stream using Velvet.	Dec 14	martinah...@gmail.com
	assemble_tag_contigs	Assemble tag contigs from overlapping BED type records in the stream.	Sep 2009	martinah...@gmail.com
	bin_vals	Bins values to a specfied key from records in the stream.	Sep 2010	martinah...@gmail.com
	bioscript	Enable Perl scripting on the data stream.	Nov 2010	martinah...@gmail.com
	biostat	Monitor status of running Biopieces.	Nov 2009	martinah...@gmail.com
	blast_seq	BLAST sequences in the stream against a specified database or genome.	Mar 2010	martinah...@gmail.com
	blast_seq_pair	BLAST a pair of sequences in the stream against each other.	Jun 2011	martinah...@gmail.com
	blat_seq	BLAT sequences in the stream against a genome.	Mar 2010	martinah...@gmail.com
	bowtie_seq	Use Bowtie to map sequences in the stream against a specified or genome or index.	Oct 2010	martinah...@gmail.com
	bwa_seq	Use BWA to map sequences in the stream against a specified or genome or index.	Sep 2009	martinah...@gmail.com
	calc_N50	Calculate N50 for sequences in the stream.	Feb 2011	martinah...@gmail.com
	calc_bit_scores	Calculate the bit score for each position based on an alignment in the stream.	May 2009	martinah...@gmail.com
	calc_density	Count BED entries or accumulate SCOREs of BD entries within each sliding window over chromosome.	Dec 2010	martinah...@gmail.com
	calc_fixedstep	Calculate fixedstep entries from records in the stream.	Sep 2009	martinah...@gmail.com
	cat_seq	Concatenates sequences in the stream and outputs a record with this sequence.	Jun 2011	martinah...@gmail.com
	clip_adaptor	Clip sequences in the stream based on ADAPTOR_POS key.	May 2011	martinah...@gmail.com
	clip_seq	Clip sequences in the stream based on soft masked sequences.	Mar 2011	martinah...@gmail.com
	complement_seq	Complement nucleotide sequences in the stream.	May 2009	martinah...@gmail.com
	compute	Performs computations on records in stream.	Jan 3	martinah...@gmail.com
	count_records	Count the number of records in the stream.	Apr 2011	martinah...@gmail.com
	count_vals	Count the number of times values of given keys exists in stream.	May 2009	martinah...@gmail.com
	create_blast_index	Create a BLAST index from sequences in stream for use with [blast_seq].	Oct 2009	martinah...@gmail.com
	create_bowtie_index	Create a Bowtie index from sequences in stream for use with [bowtie_seq].	Oct 2009	martinah...@gmail.com
	create_bwa_index	Create a BWA index from sequences in stream for use with [bwa_seq].	Sep 2009	martinah...@gmail.com
	create_fixedstep_index	Create an index from fixedstep entries in the stream for use with [get_fixedstep].	Jun 2010	martinah...@gmail.com
	create_seq_index	Create an index from sequences in stream for use with [get_seq].	Sep 2009	martinah...@gmail.com
	create_vmatch_index	Create a Vmatch index from sequences in stream for use with [vmatch_seq].	Jul 2009	martinah...@gmail.com
	create_weight_matrix	Create a residue composition weight matrix of an alignment in the stream.	May 2009	martinah...@gmail.com
	denoise_seq	Denoise sequences with quality scores in the stream.	Apr 18	martinah...@gmail.com
	digest_seq	Split sequences in the stream at a given restriction enzyme's cleavage sites.	Jan 2011	martinah...@gmail.com
	duplicate_record	Duplicate records in the stream using the value to a specified key.	Feb 23	martinah...@gmail.com
	embl_index	Scan EMBL files and output file indexing information.	Jul 2009	martinah...@gmail.com
	extract_seq	Extract subsequence from sequences in stream.	May 2010	martinah...@gmail.com
	find_SNPs	Find SNPs in SAM type records in the stream.	Sep 2011	martinah...@gmail.com
	find_adaptor	Find adaptors or part thereof in sequences in the stream.	May 2011	martinah...@gmail.com
	find_barcodes	Find and remove barcodes in sequences in the stream.	Oct 2011	martinah...@gmail.com
	find_gaps	Find gaps in sequences in the stream.	Jan 2011	martinah...@gmail.com
	find_genes	Find genes in prokaryotic genomic sequences in the stream.	Nov 14	martinah...@gmail.com
	find_homopolymers	Find homopolymers in sequences in the stream.	Dec 2010	martinah...@gmail.com
	findsim_seq	Find similar sequences between query sequences from the stream and a database.	May 8	martinah...@gmail.com
	flip_tab	Flip table records so rows becomes columns and visa versa.	May 2009	martinah...@gmail.com
	fold_seq	Fold sequences in stream.	May 2009	martinah...@gmail.com
	format_genome	Format a genome creating specified indexes.	Sep 2009	martinah...@gmail.com
	get_embl_entry	Get an EMBL entry from the MySQL database and flatfiles.	Aug 2009	martinah...@gmail.com
	get_fixedstep	Extract fixedstep values from an indexed fixedstep file.	Jun 2010	martinah...@gmail.com
	get_genome_align	Extract alignments from a multiple genome alignment.	Jun 2009	martinah...@gmail.com
	get_genome_phastcons	Extract phastcons scores ifrom a specified genome.	Jun 2009	martinah...@gmail.com
	get_genome_seq	Extract subsequences from a genome sequence.	May 2009	martinah...@gmail.com
	get_seq	Extract a subsequence from an indexed sequence.	Sep 2009	martinah...@gmail.com
	grab	Grab records in stream.	Jul 2009	martinah...@gmail.com
	head_records	Emit the only the first number of records in the stream.	May 2009	martinah...@gmail.com
	hmmer_seq	HMMER search sequences in the stream against a specified database.	May 3	martinah...@gmail.com
	indel_seq	Introduce indels into sequences in the stream.	Sep 2011	martinah...@gmail.com
	intersect_records	Intersect records in the stream based on overlapping intervals contained in values to specific keys.	Jan 2010	martinah...@gmail.com
	invert_align	Inverts an alignment showing only non-mathing residues using the first sequence as reference.	May 2009	martinah...@gmail.com
	join_seq	Join sequences in the stream.	Sep 2011	martinah...@gmail.com
	kmer_freq	Determine the frequencies for k-mers in sequences in the stream.	Feb 2011	martinah...@gmail.com
	length_seq	Determines the length of each sequence in the stream.	Sep 2010	martinah...@gmail.com
	length_vals	Find the length of values in the stream for given keys.	May 2009	martinah...@gmail.com
	list_biopieces	Print summary for all Biopices.	May 2009	martinah...@gmail.com
	list_genomes	Display available genomes.	May 2009	martinah...@gmail.com
	list_mysql_databases	Display all MySQL databases.	Jul 2009	martinah...@gmail.com
	lowercase_seq	Lowercases sequences in stream.	Jul 2009	martinah...@gmail.com
	mask_seq	Mask sequences in the stream based on quality scores.	Dec 5	martinah...@gmail.com
	match_seq	Find all matches between sequences in the stream.	Sep 2009	martinah...@gmail.com
	mate_pair_dist	Determines the distance between mapped mate-pair sequence matches.	Feb 2011	martinah...@gmail.com
	max_vals	Find the maximum values in the stream for given keys.	Oct 2010	martinah...@gmail.com
	mean_scores	Calculate the mean or local mean of quality SCORES in the stream.	May 2011	martinah...@gmail.com
	mean_vals	Find the mean values in the stream for given keys.	Oct 2010	martinah...@gmail.com
	median_vals	Find the median values in the stream for given keys.	Oct 2010	martinah...@gmail.com
	merge_records	Merge records in the stream based on identifier values to specific keys.	May 2009	martinah...@gmail.com
	merge_vals	Merge values of keys in a record.	Nov 10	martinah...@gmail.com
	min_vals	Find the minimum values in the stream for given keys.	Oct 2010	martinah...@gmail.com
	mutate_seq	Introduce mutations into sequences in the stream.	Aug 2011	martinah...@gmail.com
	oligo_freq	Determines the oligo frequencies of sequences in stream.	May 2009	martinah...@gmail.com