Banana Slug Genomics

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===== SOAPdenovo =====

==== Overview ====

SOAP = Short_Oligonucleotide_Analysis_Package\\
SOAPdenovo assembles short oligonucleotide into contigs and scaffolds
for de-novo assembly of short-reads using de Bruijn graphs.\\
Can use a hierarchy of sizes of paired-end data.\\
Has been successfully used to sequence the Panda and Human genomes.\\
Quality seems good.  They ran Panda genome on 256GB workstation with 32 CPUs.

There is a [[http://soap.genomics.org.cn/soapdenovo.html|description]] which contains a
download link.

Created by BGI - Beijing Genomics Institute [[http://en.wikipedia.org/wiki/Beijing_Genomics_Institute|wiki]].

**The sequence and de novo assembly of the giant panda genome**
[(cite:panda>
The sequence and de novo assembly of the giant panda genome
Nature 463, 311-317 (21 January 2010)\\
doi:[[http://dx.doi.org/10.1038/nature08696|10.1038/nature08696]];\\
Received 19 August 2009; Accepted 24 November 2009; Published online 13 December 2009
)]




Downloaded the binaries for SOAPdenovo and [[http://soap.genomics.org.cn/about.html#resource2|GapCloser]]. I copied these binaries to the /bin folder since there are only two, and they at least correctly display a help message when you run them without arguments.



==== Website ====
[[http://soap.genomics.org.cn/soapdenovo.html]]

==== Source with Binaries and Documentation ====
[[http://soap.genomics.org.cn/down/]]

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

Banana Slug Genomics

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