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Question: De novo assembly of a genome sequence
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gravatar for yzhang
3.7 years ago by
yzhang • 0
United States
yzhang • 0 wrote:

I am new to the Galaxy. Can you do a de novo sequence asembly using the Galaxy? Thanks.
assembly genome galaxy • 1.6k views
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modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by yzhang • 0
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gravatar for fubar
3.7 years ago by
fubar ♦ 1.1k
Australia
fubar ♦ 1.1k wrote:

For assembling small (eg prokaryote) genomes you could try out https://orione.crs4.it/ and work through the tutorials at https://github.com/emarinier/PUBS2015/blob/master/Section1/Section1.md - that first one includes assembly with abyss.

You will probably need a local or cloud instance with dedicated resources for larger genome assembly because it's too resource intensive to be offered as a free public service AFAIK. All of the Galaxy tools exposed at orione are freely available at  https://bitbucket.org/crs4/orione-tools/src/f6fef89f1a85/custom/?at=bb-orione-tools for local installation.
ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by fubar ♦ 1.1k
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