Screenshots:

Requirements:

• velvet (velveth,velvetg should be in your PATH)
• R (with Sweave, usually included)
• R libraries (from R prompt type install.packages("ggplot2","proto","xtable"))
• pdflatex (usually part of TeTeX)
• Perl (with PerlIO::gzip)

Optional:

• To generate alignments against a reference genome, use either
• BLAT (add to your PATH)
• BLAST (add to your PATH)

To Download:

• Get Subversion
• svn checkout http://standardized-velvet-assembly-report.googlecode.com/svn/trunk/ standardized-velvet-assembly-report-read-only

To Run:

• Edit permute.sh to your liking, paying particular attention to the kmer, cvCut, expCov, and other crucial flags like shortPaired
• perl fastaAllSize mysequences.fa > mysequences.stat
• ./permute.sh mysequences (leave out the .fa)

• If NOT using a reference genome skip this section
• If using Blat:
• faToTwoBit myrefgenome.fa myrefgenome.2bit
• gfServer start localhost 9999 myrefgenome.2bit
• for f in out*dir; do if [ ! -e $f/contigsVsRef.psl ]; then echo $f; gfClient localhost 9999 ./ $f/contigs.fa $f/contigsVsRef.psl; fi; done
• If using BLAST:
• formatdb -i myrefgenome -p F
• for f in out*dir; do if [ ! -e $f/contigsVsRef.m8 ]; then echo $f; blastall -i $f/contigs.fa -p blastn -d myrefgenome -m 8 -o $f/contigsVsRef.m8; fi; done

• for f in out*dir; do if [ ! -e $f/metadata.txt ]; then perl generateAssemblyStats.pl $f > $f/metadata.txt; fi; done
• for f in out*dir; do echo "groupDir<-\"$f\";statFile<-\"mysequences\";statTab<-\"$f/stats.txt\";metaTab<-\"$f/metadata.txt\";source(\"calculateStats.R\")" | R --no-save --quiet; done

• Choose one of three report formats
• If you wish to skip the individual contig length histograms (much quicker)

echo "assmName<-\"mysequences\";statFile<-\"mysequences\"; Sweave(\"shortReport.Rnw\",output=\"mysequences.tex\");" | R --no-save --quiet

• If using no reference genome:

echo "assmName<-\"mysequences\";statFile<-\"mysequences\"; Sweave(\"report.Rnw\",output=\"mysequences.tex\");" | R --no-save --quiet

• If using the reference genome alignments:

echo "refName<-\"My reference genome\";assmName<-\"mysequences\";statFile<-\"mysequences\"; Sweave(\"refReport.Rnw\",output=\"mysequences.tex\");" | R --no-save --quiet

• pdflatex mysequences.tex
• View the pdf report mysequences.pdf