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christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
68 stars 9 forks source link

choice of aligner? #22

Closed tamburinif closed 6 years ago

tamburinif commented 6 years ago

Hi there, just wondering why alignments have to be performed with Bowtie2. Would using BWA be okay?

christophertbrown commented 6 years ago

Hi Fiona,

I have only used and tested iRep with Bowtie2, but in theory it should work with any mapper that has standardized SAM output.

Chris

On Jun 20, 2018, at 11:25 PM, Fiona Tamburini notifications@github.com wrote:

Hi there, just wondering why alignments have to be performed with Bowtie2. Would using BWA be okay?

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tamburinif commented 6 years ago

Thank you for the information and quick reply, Chris!