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Sequence alignment with MAFFT or Muscle #3

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rvosa opened this issue Apr 11, 2020 · 1 comment
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Sequence alignment with MAFFT or Muscle #3

rvosa opened this issue Apr 11, 2020 · 1 comment
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@rvosa
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rvosa commented Apr 11, 2020 •
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The experiences detailed here (nextstrain/ncov#268) show that doing the MSA in one big run eventually becomes prohibitive. This was not a problem for the 400 GenBank genomes set, but as those submissions are increasing (or when we add GISAID data) it becomes an issue.

MAFFT has the virtue of being the standard that is now being used (e.g. by Rambaut et al.) but it might be slower than Muscle (@rvosa's subjective experience)? Both can be run on the CIPRES cluster. Test and decide.
@rvosa rvosa added this to the Full workflow milestone Apr 11, 2020
This was referenced Apr 11, 2020
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@rvosa rvosa changed the title Decide on alignment: MAFFT vs Muscle, decomposed or one big run? Sequence alignment with MAFFT or Muscle Apr 11, 2020
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rvosa commented Apr 13, 2020 •
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cipresrun \
     -y data/cipres_appinfo.yml \
     -t MAFFT_XSEDE \
     -p vparam.anysymbol_=1 \
     -i data/genomes/sars-cov-2.fasta \
     -o data/genomes/output.mafft

@rvosa rvosa closed this as completed Apr 13, 2020
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