Hello.
I use SOLiD de novo pipeline (http://solidsoftwaretools.com/gf/project/denovo/) to assemble bacterial genome.
I use Mummerplot for proof-mapping the resulting contigs to reference genome. Double-encoded contigs (contigs.de) look OK. However, after they are converted to base-space by ASiD utility, they break apart into small pieces, see figures. Single contig is double-encoded, while multiple fragments are what it turns into in base-space.
Anybody has a suggestion on how to cure this problem?
PS: I tried older version of SOLiD pipeline (denovo_preprocessor_solid + velvet + denovo_postprocessor_solid + denovoadp) and the base-space contigs were uncorrupted. However, it is much slower, so I'd still like to fix the latest denovo tool.
I use SOLiD de novo pipeline (http://solidsoftwaretools.com/gf/project/denovo/) to assemble bacterial genome.
I use Mummerplot for proof-mapping the resulting contigs to reference genome. Double-encoded contigs (contigs.de) look OK. However, after they are converted to base-space by ASiD utility, they break apart into small pieces, see figures. Single contig is double-encoded, while multiple fragments are what it turns into in base-space.
Anybody has a suggestion on how to cure this problem?
PS: I tried older version of SOLiD pipeline (denovo_preprocessor_solid + velvet + denovo_postprocessor_solid + denovoadp) and the base-space contigs were uncorrupted. However, it is much slower, so I'd still like to fix the latest denovo tool.
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