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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 - [[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. ==== INSTALLING SOAPdenovo ==== 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~~
Discussion
I ran SOAPdenovo on the 454 Pog reads. I tried all 5 versions of SOAPDenovo that are available, and none of them can read even the simplest FASTA file, despite all the documentation saying that it is supported. The only other format it shows is FASTQ, so I found a free program that converts SFF to FASTQ and ran that. After it was done, SOAPdenovo largest contig it made was only 4k. And just like with velvet, it actually does better with the data from set1 or 2, but with both 1 and 2 454-data, it actually performs worse, i.e. smaller contigs are generated. Seems unexpected.
I now think it might read a fasta if you also provide a quality file. It perhaps cannot use fasta alone.