broadinstitute / poasta

Fast and exact gap-affine partial order alignment
BSD 3-Clause "New" or "Revised" License
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Output a row-column MSA as FASTA from our POA graph #14

Closed lrvdijk closed 8 months ago

lrvdijk commented 1 year ago

To compare the output to other tools, and for downstream analyses, it's useful to output the POA graph as a row-column MSA in FASTA format.

The choice of topological sort algorithm influences how the row-column MSA will look like. It might be worthwhile to see what other tools are doing (SPOA, ...). See also https://simpsonlab.github.io/2015/05/01/understanding-poa/

lrvdijk commented 1 year ago

Some test FASTAs one could compare to have been committed to the tests directory