pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
367 stars 40 forks source link

Be smoother with the ANI filter in the mapping step #397

Closed AndreaGuarracino closed 5 months ago

AndreaGuarracino commented 5 months ago

With low -p, the mapper was forced to examine lots of hits with little shared k-mers, increasing both runtime and memory. We avoid applying a too big filter with higher divergence.