ConFindr v0.8.1

Changelog

0.8.1 - 2023-05-19

This is a major release.

Added

• Integrated congruency of SNVs within paired-end reads into contamination calculations (a1744a4).
• Base cutoff values are now dynamically calculated based upon gene-specific quality score, length, and depth of coverage, with a starting cutoff of 3 which can be changed using --base_cutoff (880445d, 84b7d91, c06d438).
• Option to download rMLST databases using -u/--unverified within the confindr_database_setup command, for downloading databases behind a firewall and/or have a self-signed certificate.

Changed

• Refactored code by moving methods to methods.py (a7e9af6).
• Improved README.md and MkDocs documentation with increased accuracy and readability.
• Pytest tests now use downsampled samples from the originally published ConFindr benchmarking dataset, and instructions for running these tests have been added to the MkDocs (cc27c94).
• Enforced Phred33 encoding for bbduk.sh calls to support future development with Nanopore reads (#39) (ac3b976).

Removed

• Percentage contamination reporting; this was found to be unreliable and sometimes misleading (ec3ae7a).
• --cross_details flag; analysis is now always continued after cross-genus contamination has been detected (ec3ae7a).

Fixed

• TypeError that occurred when using an older version of BioPython (#27, #30, #38, #41) (19d0d1d, 96e1c7d).
• Error in install.md which suggested that rMLST databases are freely available to all users (a1ce7dc).

ConFindr v0.7.1

A few new features:

• A flag called --cross_details has been added. Previously, ConFindr would stop analysing a sample if cross contamination was detected. With this flag activated, ConFindr will continue analysis so you can get an estimate of the level of contamination.
• You can now call ConFindr just by typing confindr instead of using confindr.py (but both still work!)