How to use de novo assembly to build onto an existing reference-guided assembly.

Question

[Pryce Michener]

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?

Answer 1

[h.mon]

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

[ant_genome]

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

[h.mon]

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.