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.


Velvet has support for COLORSPACE, possibly the only de-novo short-read DBG assembler that does at this time.

Velvet has support for long-read data.

=== 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/


de-novo Tools for velvet from ABI for Solid.
http://solidsoftwaretools.com/gf/project/denovo/

=== Color-Space ===

== DE double-encoded ==
This is done by the pre-processor.
The primer base from the colorspace read is 
removed, followed by the first color, since
it was tied to the primer-base. 
In the case of mate-paired reads,
the F3 read is reversed.
Then the colors are all converted to bases
for software that doesn't parse colorspace inputs.
Thus double-encoded means reads encoded in colorspace,
and then re-encoded as if bases in base-space.

== colorspace programs ==

denovo_preprocessor
converts colorspace reads into double-encoded 24-base reads
that can be given to velvet_de.

velveth_de
colorspace version of velveth hashes reads.

velvetg_de
colorspace version of velvetg creates de Bruijn graph.

denovo_postprocessor
converts velvet output double-encoded to colorspace contigs.

denovo_adp - adapter program converts colorspace 
to base-space while reducing read errors in colorspace as much as possible.
Banana Slug Genomics

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