add read mapping option to gfastats?

vgl-hub / gfastats

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

MIT License

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add read mapping option to gfastats? #46

Closed maxmaronna closed 6 months ago

maxmaronna commented 9 months ago

Hello, Is it possible to add a read mapping strategy (ex, backmap or merqury) to gfastats? I think it would be very useful to evaluate assembly correctness.

Cheers maxmaronna

gf777 commented 9 months ago

Hi @maxmaronna Many thanks for reaching out! It would be extremely interesting to know/discuss which specific features would be more useful. Note that we have two separate tools dedicated to analyzing reads alignments to the graph and kmers (which generates QV estimates as in Merqury): https://github.com/vgl-hub/gfalign (alignment) https://github.com/vgl-hub/kreeq (kmer) Happy holidays