1.2.0

Improve within-block alignments

Cigar strings from minimap or mmseqs2 are now used to inform within-block banded alignments when merging two blocks. The cigar string, together with alignments of the two merge candidates, are used to determine mean shift and bandwidth of the banded alignment. This results in more accurate alignments.

We added two extra options for the pangraph build command, which can be used to improve the quality of the block alignments at the cost of computation time and memory usage:

• --extra-band-width: this option allows to increase the extra bandwidth of within-block banded alignments.
• --max-alignment-attempts: this option allows to increase the number of attempts to align two blocks, each attempt having increased bandwidth.

Fix handling of unaligned nodes

Occasionally, merging of two blocks could generate nodes whose alignment consists only of insertions or deletions, and no nucleotides aligned to the consensus. These problematic nodes are now detected, extracted from the block and stored in a separate singleton block, that can be further processed during graph construction.

Fix band hit warnings in Nextclade aligner

Nextclade would trigger a "band hit" warning whenever trailing indels were present. This caused performance loss.

Fix in-dels tracking

Leading in-dels were misplaced in the cigar string for matches with reverse orientation

Improve error reporting

Errors that occur during postorder traversal of the guide tree are reported immediately, without waiting for the whole tree to be traversed.

Installation and usage 📚 Documentation: docs.pangraph.org 📥 Standalone native executables: download using links in the "Assets" section just below 🐋 Docker images: neherlab/pangraph