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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
genomicswolf • 20
genomicswolf • 20 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
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modified 2.5 years ago by Devon Ryan ♦ 89k • written 2.5 years ago by genomicswolf • 20

Hello genomicswolf!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLY • link written 2.5 years ago by Michael Dondrup ♦ 46k
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gravatar for Devon Ryan
2.5 years ago by
Devon Ryan ♦ 89k
Freiburg, Germany
Devon Ryan ♦ 89k 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 COMMENT • link written 2.5 years ago by Devon Ryan ♦ 89k
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