Banana Slug Genomics

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===== VELVET =====

==== Overview====
Velvet was developed by Daniel R. Zerbino and Ewan Birney.

**Velvet: algorithms for de novo short read assembly using de Bruijn graphs** 
[(cite:velvet>Daniel R. Zerbino and Ewan Birney.\\
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs\\
Genome Res. May 2008 18: 821-829; Published in Advance March 18, 2008, \\
doi:[[http://dx.doi.org/10.1101/gr.074492.107|10.1101/gr.074492.107]]
)]

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

On wikipedia: [[wp>Velvet_(software)|Velvet]].

[[http://www.ebi.ac.uk/training/ftp/PhDtheses/Daniel_Zerbino.pdf|Daniel Zerbino's PhD Thesis on 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.

==== 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.

[[http://solidsoftwaretools.com/gf/project/denovo/|De-novo Tools for velvet from ABI for Solid]]

==== Running ====

Strategy: 
  - Find the right value for k.  For short reads remember to keep k small for good kmer coverage.
  - Find the right values for exp_cov and cov-cutoff. This is very important.
  - If you only have long reads, use them also as your short reads.

For 454 long reads, 
Final graph has 1484 nodes and n50 of 48088, max 135010, total 2464896, using 778281/782604 reads

==== Installing ====

  ssh campusrocks.cse.ucsc.edu
  
  cd /campusdata/BME235/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/


==== Examples ====

[[http://kevin-gattaca.blogspot.com/2009/12/de-novo-assembly-with-abi-solid-reads.html|example of using velvet with solid]]

==== Website ====
[[http://www.ebi.ac.uk/~zerbino/velvet/]]

==== Source with Binaries and Documentation ====
[[http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.62.tgz]]

===== References =====
<refnotes>notes-separator: none</refnotes>
~~REFNOTES cite~~
Banana Slug Genomics

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