Easy to use local assembly programs ?
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Entering edit mode
9.3 years ago

Greetings,

I'm trying to get a sense of what people are using for local assembly. Ideally I'm looking for a tool that takes a BAM file and outputs a fasta for a region of interest.

EDIT:

I'm working with whole genome data.

local-assembly • 2.2k views
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Entering edit mode
9.3 years ago
Erik Garrison ★ 2.4k

Look no further than Scalpel.

I've hacked out the microassembler component of scalpel. It does basically what you're describing except it produces an assembly graph from the BAM file in a particular region.

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9.2 years ago

The latest version of Abyss can take a paired-end BAM file as input.

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