Easy to use local assembly programs ?
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.
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Zev.Kronenberg
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2 answers
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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Erik Garrison
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Erik Garrison
The latest version of Abyss can take a paired-end BAM file as input.
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