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.
The colorspace version of velvet (_de) expects all data to be double-encoded. Mixed-space not directly supported.

Velvet has support for long-read data.

Velvet will accept sequence data from fastq input files, but does not use the quality information.

==== 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.
    * velvet-estimate-exp_cov.pl out/stats.txt makes a useful graph.
  - If you only have long reads, use them also as your short reads.

For 454 long reads, this was our best result:
  velveth out 31 -short 454/?.TCA.454Reads.fna -long 454/?.TCA.454Reads.fna
  velvetg out -exp_cov 60 -cov_cutoff 13
  Final graph has 1755 nodes and n50 of 41723, max 142286, total 2468925, using 778257/782604 reads


==== Failures ====

=== VelvetOptimiser ===
The contributed (velvet/contrib/) utility VelvetOptimiser is intended to help find 
the critical parameters k, exp_cov, and cov_cutoff.  However although it found k,
it got stuck on a local maximum on coverage and failed to produce anything useful.

=== pseudoFlow ===
Wondering if homopolymer errors in 454 data could cause trouble for the DBG,
I made a utility called pseudoFlow.c that takes all homopolymers longer than 
6 and shortens them to 6.  We know that in the range 1 to 6, 454 is accurate.
In any case, the pseudoFlow version of the data did not perform better,
in fact it was a little worse.

==== 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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