Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes

Résumé fourni par la source

Added --long-reads/--long-reads-list and --long-read-type arguments for supplying long-read (e.g. Nanopore) sequences alongside short reads. Long reads are piped through SingleM and merged into the matched short-read sample's marker gene profile, contributing to coassembly clustering decisions, then are combined with the matched short reads for Aviary assembly and recovery. Long-read samples without a matching short-read sample are also supported, contributing to clustering and being assembled/recovered with Aviary using long reads alone --sra-long-reads/--sra-long-reads-list arguments for downloading long-read-only samples directly from SRA/ENA by run accession, and --short-long-read-pairs (a TSV file of sample/long_reads pairs, each value a local file or SRA/ENA accession) for explicitly matching a long read to an existing --forward/--reverse/--sra sample, bypassing the automatic filename-based matching used by --long-reads Changed Minimum Aviary version bumped to 0.13.3, which updates CoverM to 0.8.0 and fixes long-read coverage calculation failing with "Cannot continue without minimap2" during Aviary recovery Updated SingleM to v0.21.4, fixing a DIAMOND hanging bug (#223). Thanks @megan-a-wallace for reporting

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