Question: How to use de novo assembly to build onto an existing reference-guided assembly.
gravatar for Pryce Michener
4.8 years ago by
Memphis, TN
Pryce Michener10 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 • 1.7k views
ADD COMMENTlink modified 4.8 years ago by h.mon32k • written 4.8 years ago by Pryce Michener10
gravatar for h.mon
4.8 years ago by
h.mon32k wrote:

You could try MITObom or Arc, using your drafts as starting points.

ADD COMMENTlink written 4.8 years ago by h.mon32k

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

ADD REPLYlink written 4.7 years ago by ant_genome0

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 REPLYlink written 4.7 years ago by h.mon32k
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