Sierra 3.5.1

Bugfixes:

1. Fixed a bug that failed to exclude low quality alignment from the final results (hivdb/sierra-core@95a442d)
2. Fixed several bugs that related to genotyper/subtyper.
3. Fixed an issue that missing DRPs are not reported by NGS program (hivdb/hivfacts@13b743c)

Sierra 3.5.0

HIVDB algorithm 9.6: This latest algorithm update incorporates significant modifications and enhancements in the rules and comments for NRTI, NNRTI, INSTI, and PI drug classes. A detailed comparison between algorithm versions 9.3 and 9.6 can be found in this zip file: algV9.6.zip.

Sierra 3.4.13

Bugfix: Fix a bug that MINIMAP2 argument -w 5 was accidentally removed by the previous version 3.4.12.

Sierra 3.4.12

Bugfixes:

1. Previously, minimizer window size=5 (-w 5) was employed for aligning HIV-1 sequences by minimap2. We changed this config to minimizer k-mer length=10 (-k 10 -w 5) for increase alignment sensitivity for super short sequences.
2. (3.4.11, forgot to release) Address an issue that certain CRFs were incorrectly called due to an insufficient regional subtyping rule, or a misconfiguration of region subtype (X29).

Sierra 3.4.10

HIVDB-HIV2 algorithm 9.0: Comments update since 2020.

Sierra 3.4.9

Subtyping/genotyping updates:

Subtype A is divided into A1/3/4/6/7. Two reference sequences of subtype A8 are added (MW353966/MW353967). Subtypes of six reference sequences are changed from A to X22 (CRF22_01A1) after further re-analysis is performed: AH011123, AY371167, EU743963, JN864048, KP109498, and KU168256.

Sierra 3.4.8

• HIVDB algorithm 9.5.1: Minor comments update.
• Bugfix: Certain mixtures with DRMs, for example RT:K70HN, was mistyped as "Other" mutations. This version fixed the bug.

Sierra 3.4.7

Mutation types: re-assess mutation types for non-DRM mutations. See GitHub update for details.

Sierra 3.4.6

Bugfix: Fixed a bug that prevented the program from creating a list of ambiguous mutations by filtering.

Sierra 3.4.5

• HIVDB algorithm 9.5.0: New drug resistance scores for CAI mutations; minor comments update.
• Bugfix: The TSM and SDRM drug class of an ambiguous mutation containing a TSM/SDRM AA was null. This bug has been fixed.