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Question: How to use de novo assembly to build onto an existing reference-guided assembly.
0
gravatar for Pryce Michener
4.6 years ago by
Pryce Michener • 10
Memphis, TN
Pryce Michener • 10 wrote:

I recently used the published carrot mitochondrial genome as a reference to assemble draft mitochondrial genomes for 28 of the species that I study from raw Illumina HiSeq reads. The results came out really well, but I'm getting a lot of gaps in the assemblies. I was wondering what the best way would be to run my raw reads back against these draft mitochondrial genomes and scaffold out into the gaps so that I could get more contiguous genomes. Does anyone have any advice on what the best way to do this is?
assembly de novo • 1.6k views
ADD COMMENT • link •
modified 4.6 years ago by h.mon ♦ 31k • written 4.6 years ago by Pryce Michener • 10
1
gravatar for h.mon
4.6 years ago by
h.mon ♦ 31k
Brazil
h.mon ♦ 31k wrote:

You could try MITObom or Arc, using your drafts as starting points.
ADD COMMENT • link written 4.6 years ago by h.mon ♦ 31k

does MITObim really work? I have tried, but fail for some region has very high coverage.

ADD REPLY • link written 4.5 years ago by ant_genome • 0

I had moderately good results with MITObim, better than fishing for mitochondrial contigs on full assembly, but never got a full mt genome assembled. I never got Arc to run successfully, in reality, and just gave up.

ADD REPLY • link written 4.5 years ago by h.mon ♦ 31k
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