DCGenomics
commented
6 years ago My view:
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Do not assemble each time, only at the end
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Try also with metaspades and abyss
On Nov 3, 2017 16:30, "janpb" notifications@github.com wrote:
megahit splits larger contigs when extending. I suspect it's because of the kmer approach. The current approach and logic to extend contigs is based on on overlaps.
Approaches:
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Assembling only the flanking sequences and corresponding aligned reads from magicblast, not the whole contig. The extension would be the concatenation of the extended flanks to the contig, i.e. fake a short read.
Collect reads used in the assembly and assemble reads instead of keeping a contig. However, megahit stores reads in a binary format which requires to write a special reader.
rather convoluted approach: map all reads back to contig and keep those which mapped.
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megahit splits larger contigs when extending. I suspect it's because of the kmer approach. The current approach and logic to extend contigs is based on on overlaps.
Approaches:
Assembling only the flanking sequences and corresponding aligned reads from magicblast, not the whole contig. The extension would be the concatenation of the extended flanks to the contig, i.e. fake a short read.
Collect reads used in the assembly and assemble reads instead of keeping a contig. However, megahit stores reads in a binary format which requires to write a special reader.
rather convoluted approach: map all reads back to contig and keep those which mapped.