Wednesday 22 February 2012

standardized-velvet-assembly-report - a set of scripts and a Sweave report used to iterate through parameters and generate a report on Velvet-generated sequence assemblies - Google Project Hosting

where was this when I was playing with Velvet?

a set of scripts and a Sweave report used to iterate through parameters and generate a report on Velvet-generated sequence assemblies - Google Project Hosting

http://code.google.com/p/standardized-velvet-assembly-report/

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:

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

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