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NCBI-Hackathons / NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies
MIT License
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Multiple Sequence Alignment tool? #3

Closed jcoliver closed 7 years ago

jcoliver commented 7 years ago

MAFFT may be able to handle considerably longer sequences than 10kb: http://mafft.cbrc.jp/alignment/software/tips.html#longsequences Perhaps windows could be entire chromosomes? #2 But also see note in MAFFT documentation: "Note that MAFFT assumes that the all input sequences share the order of homologous sites or blocks. If the sequences have repeat or inversion, use other tools such as FASTA and MUMmer." [emphasis added]

The suggested alternative MUMmer could be another option, but there is a steeper learning curve, and it is not clear if it is doing multiple sequence alignment or just several pairwise alignments.

jcoliver commented 7 years ago

Closing, as the parallelization of MAFFT seems to work fine.