Banana Slug Genomics

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===== VELVET =====
====High Level Overview====
Velvet was developed by Ewan Birney and Daniel R. Zerbino for de-novo assembly of short-reads using de Bruijn graphs.

Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. (2008) 18:821–829.
[[http://nar.oxfordjournals.org/cgi/ijlink?linkType=ABST&journalCode=genome&resid=18/5/821|Free full text]]

Velvet may be downloaded free from [[http://www.ebi.ac.uk/~zerbino/velvet/|here]] (GPL license).

There is a [[http://en.wikipedia.org/wiki/Velvet_(software)|wiki article]] about velvet.


== Installing ==

  ssh campusrocks.cse.ucsc.edu
  
  cd /campusdata/BME235/programs
  # but currently having problems with my group membership
  #cd $HOME
  # mkdir programs
  # cd programs
  # 
  wget http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.62.tgz
  tar xfz velvet_0.7.62.tgz
  mv velvet_0.7.62 velvet
  mv velvet_0.7.62.tgz velvet/
  cd velvet
  make
  make color
  # color versions work with solid, have _de extension
  # install to bin dir
  cp velveth velvetg velveth_de velvetg_de /campusdata/BME235/bin/

Banana Slug Genomics

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