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?
Question: How to use de novo assembly to build onto an existing reference-guided assembly.
3.1 years ago by
Pryce Michener • 10
Pryce Michener • 10 wrote:
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