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Published June 15, 2021 | Version v0.3.0
Software Open

TRON-Bioinformatics/covigator-ngs-pipeline: Release Covigator NGS pipeline v0.3.0

Creators

  • 1. @TRON-Bioinformatics

Description

Major changes

  • Add read trimming with fastp
  • Output QC results in JSON format
  • Integrate 4 variants callers: BCFtools, iVar, GATK and LoFreq
  • Include soft filtering of variants based on VAF for all variants from LoFreq and for indels from BCFtools
  • Integrate SnpEff 5.0 for the variant annotation
  • Parametrize some quality thresholds

Files

TRON-Bioinformatics/covigator-ngs-pipeline-v0.3.0.zip

Files (63.1 MB)

Additional details

Related works

Is supplement to
https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/tree/v0.3.0 (URL)