IPA v1.8.0

• Completely redesigned the layout stage from scratch.
• Improved contiguity.
• Output of the new version is no longer compatible with FALCON-Phase.

IPA v1.5.0

• Removed Pbmm2 for polishing. This should allow a much faster overall runtime, especially on genomes with low-complexity sequences.
• Pancake has a new maximum seed length of 28 (instead of 32 like before). This is due to a new seed data structure which encodes seed span.
• GNU time in the IPA workflow is now used only when available.
• GFA string graph is now being written at the end of the 10-assemble stage.
• Overall improvements to stability and efficiency.

Drop "-e" from purge_dups

The -e can still be added by configuration, via config_purge_dups_get_seqs.

Support .fq and other extensions

PacificBiosciences/pbbioconda#326

Support purge_dups after parallel pancake

See README.

htslib-1.10 unpinned in Bioconda

See CHANGELOG.md

Bug-fixes; retain high copy number elements

See CHANGELOG.md

Improved sharding for parallel tasks

See CHANGELOG.md