Read coverage calculator for metagenomics
GPL-3.0 License
Add CITATION.cff
Add --checkm2-quality-file
Use strobealign as default mapper, instead of minimap2
Update Galah to v0.4.0
Add minimap2-hifi (#122)
Update to clap command line parser v4
Support both BWA and BWA-MEM2 (#72). Thanks @jianshu93
genome: Update --reference
help (#111). Thanks @gallardoalba
genome: Add --use-full-contig-names
(#86). Thanks @shafferm
genome_parsing: Allow compressed genomes
contig: Always reset after each contig. Thanks @PandengWang
contig: Fix documented default for --min-covered-fraction
. Thanks Jiarui Sun
make: Detect when output filenames clash. Thanks @akiledal
filter: Detail --proper-pairs
/--invert
interactions. Thanks @Rridley7
release: Drop symbols and use lto (#129). Thanks @jakobnissen
mapping_index: Allow missing bwa-mem ref when index exists (#112). Thanks @fbeghini
Full Changelog: https://github.com/wwood/CoverM/compare/v0.6.1...v0.7.0
Published by wwood over 3 years ago
Published by wwood almost 4 years ago
$TMDIR
to change the temporary directory used (Thanks @ShangjinTan, #41)-x
so it handles a leading dot (Thanks @mcmahon-uw com, #49)Published by wwood about 4 years ago
--full-help
is displayed by making it a man page, and publishing HTML versions. Add man
as a dependency.genome
when used with --no-zeroes
that caused incorrect coverage estimates--exclude-supplementary-alignments
) (#34)genome
: Add --genome-fasta-list
input optionThanks to Rhys Newell (@rhysnewell), Jianshu Zhao (@jianshu93), Atul Bhosale (@Atul9), and Antônio Pedro Camargo (@apcamargo) for contributions to this release.
Published by wwood almost 5 years ago
Thanks to Rochelle Soo for reporting bugs fixed here.
Published by wwood almost 5 years ago
Published by wwood about 5 years ago
genome_name<tab>contig
Thanks to Rhys Newell and Mitchell Sullivan for helpful advice, and @ucassee and @jerceyli for useful feature requests.
Published by wwood over 5 years ago
Published by wwood over 5 years ago
covered_bases
and reads_per_base
are new coverage statistics (methods)--min-covered-fraction
, reads mapped to that genome are not counted as mapped when calculating relative abundance (same for contig mode).-read
to reduce potential confusionPublished by wwood over 5 years ago
Published by wwood almost 6 years ago