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Old 06-05-2015, 09:47 AM   #222
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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Hi Luc,

Tadpole does not replace BBMerge, though I plan to further integrate them in the future - mainly, so that BBMerge can first attempt to merge, then if unsuccessful extend the reads using Tadpole, then attempt to merge again, and if still unsuccessful, undo all the changes.

The main reason I made "Tadpole" was because I need to quantify the insert size of libraries, to determine whether they are acceptable; for example, if a project needs a 2x150bp library with a 500bp insert size, for an unknown organism... how do you determine whether it passes? BBMerge only works when the reads are largely overlapping. So, I wrote Tadpole to extend the right end of non-overlapping reads so that they will overlap and can be merged. So far, it works really well on 2x150bp single-cell data with a 350bp insert size, but I have not tested it further than that.

Tadpole is a complete (and very fast) assembler; you can run "tadpole.sh in=reads.fq out=contigs.fa" and it will give you a conservative assembly with a low error rate. The main drawback is that currently the max kmer length is 31, and as such the continuity is poor. I'm evaluating it for use in making a quick assembly for mapping reads to recalibrate their quality, prior to feeding them to a more sophisticated assembler; for recalibration, a low error rate and low misassembly rate is more important than continuity.

For extending reads, the command would be:
tadpole.sh in=reads.fq extend=reads.fq oute=extended.fq mode=extend extendleft=100 extendright=100

That will extend the reads by up to 100bp in each direction, stopping early if a branch is hit. For extending paired reads so that they overlap, only “extendright” is needed, so “extendleft” should be set to zero.
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