<![CDATA[BOL: Standardized velvet assembly report]]> https://bioinformaticsonline.com/bookmarks/view/30090/standardized-velvet-assembly-report? https://bioinformaticsonline.com/bookmarks/view/30090/standardized-velvet-assembly-report Fri, 09 Dec 2016 03:59:59 -0600 https://bioinformaticsonline.com/bookmarks/view/30090/standardized-velvet-assembly-report <![CDATA[Standardized velvet assembly report]]> Requirements:

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

Optional:

  • BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, add faToTwoBit,gfClient,gfServer to your PATH. If using BLAST, add blastall and formatdb.

Edit permute.sh to your liking, paying particular attention to the kmer, cvCut, expCov, and other flags

To Run:

  1. perl fastaAllSize mysequences.fa > mysequences.stat or gunzip -c mysequences.fa.gz | fastaAllSize > mysequences.stat Substitute fastqAllSize for fastq files.
  2. ./permute.sh mysequences (leave out the .fa)

https://github.com/leipzig/standardized-velvet-assembly-report

Address of the bookmark: https://github.com/leipzig/standardized-velvet-assembly-report

]]> Poonam Mahapatra