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--- archive:bioinformatic_tools:velvet [2010/04/11 00:17]
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+++ archive:bioinformatic_tools:velvet [2010/04/28 20:58]
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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.
+==== Overview====
-[[http://nar.oxfordjournals.org/cgi/ijlink?linkType=ABST&journalCode=genome&resid=18/5/821|Free full text]]
+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).
-There is a [[http://en.wikipedia.org/wiki/Velvet_(software)|wiki article]] about velvet.
+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.
-=== Installing ===
+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
+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
-  # 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
@@ Line 36: / Line 102: @@
   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~~

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