12/12/2014
Customer would like to assemble a genome but it is technically challenging to extract adequate sample from a single individual thus a pooled sample has to be used, and this species is known to have high level of diversity across individuals.
Fri, 12/12/2014 at 9:33 AM
AccuraScience LB: Many have faced challenges in either pooled samples or samples with high level of heterozygosity. There are a few potential solutions:
(1) Cortex: http://cortexassembler.sourceforge.net/. It includes a tool called cortex_con for "consensus genome assembly" with pooled samples. Cortex's reference is this Nature Genetics paper: http://www.nature.com/ng/journal/v44/n2/full/ng.1028.html. Unfortunately cortex_con is still in beta testing.
(2) Broad Institute's old tool ARACHNE includes some notes on assembling polymorphic genomes: http://www.broadinstitute.org/crd/wiki/index.php/Polymorphism that may be worth trying.
(3) BGI's new SOAPdenovo (or SOAPdenovo2) takes high heterozygosity situation into account: http://www.gigasciencejournal.com/content/1/1/18.
(4) Hapsembler is "a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism": http://compbio.cs.toronto.edu/hapsembler/.
(5) Planatus is a tool for "Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads". Reference is this Genome Research paper: http://genome.cshlp.org/content/early/2014/04/22/gr.170720.113.
(6) Abyss has been used in a similar situation: https://pag.confex.com/pag/xxiii/webprogram/Paper15404.html.
Not all of these will work, thus this work will be exploratory nature and will involve trial-and-error style testing. In the end, I think it's likely that we can get 2 or more of these tools work thus a comparison can be made.
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