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kbaseattic / assembly

An extensible framework for genome assembly.
MIT License
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implement a plugin for Pilon #234

Open levinas opened 10 years ago

levinas commented 10 years ago

Used by Broad to post-process AllPaths-LG assemblies.

http://www.broadinstitute.org/software/pilon/reference/

HOW PILON IDENTIFIES BAD LOCATIONS AND REGIONS

Pilon determines which regions may contain contiguity breaks requiring local reassembly by looking for the following motifs:

"V-dips," or locations where coverage drops significantly as compared to flanking regions General low coverage Large percentage of soft-clipped alignments at a specific locus A high percentage of invalid pairs Note that multiple such events in close proximity (~200bp) will be treated as a single suspect region.