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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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Change Bowtie version #138

Closed hcecilia closed 10 years ago

hcecilia commented 10 years ago

Hello, I guess metAMOS 1.5-rc3 works with Bowtie 1 since I've had some errors about my read lenght exceeding 1024 bp. I have Bowtie2 on my computer, which doesn't have any upper limit for read lenght. Where should I tell metAMOS to use this version ? Thank you,

skoren commented 10 years ago

MetAMOS also has support for bowtie2, you can specify a different aligner using -m bowtie2 to runPipeline. Bowtie2 does require the pysam package so if you have problems running it, check the runPipeline output for messages about missing or invalid pysam package.