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What is the fastest whole genome aligner available in Galaxy cloud software?

What is the fastest whole genome aligner available in Galaxy cloud software? Also need to choose the most precise and accurate variant callers appropriate for the Myc. tuberculosis genomes.

wgs galaxy
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updated by Devon Ryan Devon Ryan • written by genomicswolf • genomicswolf

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written by Michael Dondrup Michael Dondrup

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The fastest one in the toolshed is hisat2 (the wrapper is just called "hisat" if I remember correctly). For the "most precise variant caller" I can't really say, since that depends on settings/filtering. Freebayes is pretty good and available in Galaxy. I don't know what the state is of the GATK wrapper. That'd normally be the "go to" variant caller, but the licensing and downloading annoyance make it a little more difficult for proper Galaxy integration.

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written by Devon Ryan Devon Ryan

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