bede/hostile: 1.0.0

Published January 22, 2024 | Version 1.0.0

Software Open

Arbitrary index downloading and caching using names defined in manifest.json (see table in readme for available indexes or run hostile fetch --list). This means you can run e.g. hostile clean --index human-t2t-hla-argos985 --fastq1 reads.fq.gz and Hostile will fetch that index if you don't have it already. Addresses https://github.com/bede/hostile/issues/28
Two new standard indexes:
- human-t2t-hla.rs-viral-202401_ml-phage-202401 (RefSeq viral & Millard Lab phage)
- human-t2t-hla.argos-bacteria-985_rs-viral-202401_ml-phage-202401 (ARGOS bacteria, RefSeq viral, & Millard Lab phage)
Improved masking protocol for custom index creation (hostile mask)
- Uses minimap2 with modified secondary alignment limit and secondary-to-primary score ratio threshold (-N and -p)
- Uses dnaio to read the target genome and make 150mers with a step of 10bp by default
New options for hostile clean: --aligner-args, --invert, and --offline
Verification of downloaded index checksums in manifest.json (https://github.com/bede/hostile/issues/20)
Adds version, aligner and options fields to log output
Bugfix: when 0 reads remain after decontamination, the resulting empty fastq.gz files are no longer corrupted (https://github.com/bede/hostile/issues/24).
Disable potentially surprising fallback to Minimap2 if an error is encountered running Bowtie2
Symlinked FASTQ paths are followed but no longer resolved
Links to published article

Files

Name	Size	Download all
bede/hostile-1.0.0.zip md5:aec58fdf2637a44cb4538c122c626419	1.7 MB	Preview Download

Is supplement to: Software: https://github.com/bede/hostile/tree/1.0.0 (URL)