0.4.0 - 14/12/2022

mbhall88 released this 14 Dec 05:13

· 24 commits to main since this release

0.4.0

Added

download subcommand to download and validate the decontamination database
sorting of the decontaminated fastq file to ensure subsampling is reproducible regardless of whether a combined fastq or directory of fastqs is provided [#48]

Changed

Default (expected) location of the decontamination database is now ${HOME}/.tbpore/decontamination_db/remove_contam.map-ont.mmi
Variant filtering params
- minimum depth changed from 0 to 5
- minimum variant quality (QUAL) score from 85 to 25
- minimum mapping quality from 0 to 30

Removed

Usage of deprecated iteritems function from pandas. This will remove an annoying deprecated warning when running tbpore cluster

Assets 2