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Question: Which mapping tool is best to compare 2 E.coli genomes?
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gravatar for edwardbevan
2.3 years ago by
edwardbevan • 0
edwardbevan • 0 wrote:

Which mapping tool is best for comparing E.coli contigs to an E.coli reference genome?
bacteria galaxy comparison • 461 views
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modified 2.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by edwardbevan • 0
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gravatar for Jennifer Hillman Jackson
2.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Mappers that permit long-read inputs would be appropriate such as: Blast, BLAT, etc.

To see all mappers already wrapped for Galaxy, review the category "Next Gen Mappers" in the Tool Shed.

If the tool you wish to use is not wrapped for Galaxy yet, it could be. There are some specialize mappers for circular genomes available in the wider bioinformatic community, some proprietary, but I don't believe any have been wrapped for Galaxy yet (but we may still get more replies).

Also see this prior question at the main Biostars site: https://www.biostars.org/p/10081/

Best, Jen, Galaxy team
ADD COMMENT • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen that's useful,

BW

Ed

ADD REPLY • link written 2.3 years ago by edwardbevan • 0
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