Question: (Closed) What is the fastest whole genome aligner and variant caller?
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gravatar for vassialk
4.3 years ago by
vassialk190
Belarus
vassialk190 wrote:

What is the fastest whole genome aligner and variant caller? Tried Nextgene, CLC, Lasergene, Ugene.

Want to find a better solution for WGS mutation discovery.

Thank you.

sequencing tub wgs • 1.4k views
ADD COMMENTlink modified 4.3 years ago by Istvan Albert ♦♦ 82k • written 4.3 years ago by vassialk190
1

You'll find that there are things like BCBio-nextgen that work to parallelize your alignment/variant calling steps in an efficient manner. Give something like that a try before changing aligners too.

ADD REPLYlink written 4.3 years ago by Devon Ryan93k

Hello vassialk!

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 REPLYlink written 3.1 years ago by Michael Dondrup47k
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gravatar for Brian Bushnell
4.3 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

Looking for the fastest tool, in a field where the quality of tools varies wildly, is not really a productive exercise. For this purpose I would recommend aligning with BBMap and calling variants with samtools mpileup or GATK, which will give you quality variant calls.

ADD COMMENTlink modified 10 weeks ago by RamRS25k • written 4.3 years ago by Brian Bushnell17k
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gravatar for Istvan Albert
4.3 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

Rather than looking for the fastest you should refocus your search on finding the most accurate aligner that operates within the requirements that you have.

ADD COMMENTlink modified 10 weeks ago by RamRS25k • written 4.3 years ago by Istvan Albert ♦♦ 82k

Thx, I need a good aligner for the whole genome to whole genome contigs alignment

ADD REPLYlink written 4.3 years ago by vassialk190
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