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Published June 22, 2021 | Version v0.4.0
Software Open

TRON-Bioinformatics/covigator-ngs-pipeline: Release Covigator NGS pipeline v0.4.0

  • 1. @TRON-Bioinformatics

Description

Major changes

  • Support DNA assemblies in FASTA format as input instead of raw reads. Variant calling on the assembly is implemented using BioPython PairwiseAligner and a valid VCF is created. This VCF is then normalized and annotated with SnpEff. Thus providing a VCF compatible with the VCFs generated from the FASTQ files.
  • The variant normalization is reimplemented locally to avoid a call to Nextflow which was not efficient.

Minor changes

  • Ensure the work folder are cleaned up after correct execution
  • Add an initialization mode convenient to install the pipeline and initialize the conda environments before running on multiple samples concurrently.

Files

TRON-Bioinformatics/covigator-ngs-pipeline-v0.4.0.zip

Files (62.9 MB)

Additional details