Banana Slug Genomics

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===== SOAPdenovo =====

==== Overview ====

SOAP = **S**hort **O**ligonucleotide **A**nalysis **P**ackage\\
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 - [[wp>Beijing_Genomics_Institute]].

**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.

==== Quirks ====

=== NO FASTA, ONLY FASTQ ===
Unable to get SOAPdenovo to read any kind of FASTA file, despite
the documentation FASTA examples.  Tried many variants of the FASTA file,
even tried all 5 versions available for download, but
could not get it to work.  The other example shows the use of FASTQ.
Found and installed sff2fastq utility. Made FASTQ version of the 454 data.
Was able to get SOAPdenovo to run finally.

Perhaps it just won't take the fasta input by itself.
It might work if you include a qual file with your fasta.


==== Installing ====

  cd /campusdata/BME235/programs
  wget http://soap.genomics.org.cn/down/SOAPdenovo-v1.04.tgz
  tar xfz SOAPdenovo-v1.04.tgz
  mv SOAPdenovo_Release1.04 SOAPdenovo
  mv SOAPdenovo-v1.04.tgz SOAPdenovo/
  cd SOAPdenovo
  cp SOAPdenovo ../../bin/


==== 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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