v0.7.5

• Report now defaults to INSTRUMENT_VENDOR=Illumina (matches existing behavior of jobscript.sh)

v0.7.4

Upgrade dependencies:

• Pangolin 4.3
• Nextclade 2.14.0

Docker Image:

quay.io/refgenomics/covid19:v0.7.4

Added ARTIC V4 and V4.1 primers

The primer set used for alignment trimming can now be specified, and defaults to ARTIC V4.1.

v0.4.12

v0.4.12

Improved handling of poly-A tail

• Trims reference of polyA tail to avoid read mis-mapping
• Fixes bug in report generation causing incorrect total # of reads to be rendered in the PDF output
• Note: Consensus sequence for polyA tail is now Ns

Corresponds to job b45241df22b043a9 on One Codex.

Initial release

Initial SARS-CoV-2 pipeline with support for Illumina data, including Twist capture-based protocol, WGS, and ARTIC v1 scheme amplicon sequencing. Includes Jupyter notebook for report generation.