Question: (Closed) What is the fastest whole genome aligner available in Galaxy cloud software?
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gravatar for genomicswolf
2.5 years ago by
genomicswolf20
genomicswolf20 wrote:

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.

galaxy wgs • 741 views
ADD COMMENTlink modified 2.5 years ago by Devon Ryan89k • written 2.5 years ago by genomicswolf20

Hello genomicswolf!

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Not a real question

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ADD REPLYlink written 2.5 years ago by Michael Dondrup46k
1
gravatar for Devon Ryan
2.5 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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.

ADD COMMENTlink written 2.5 years ago by Devon Ryan89k
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