Published June 22, 2021
| Version v0.4.0
Software
Open
TRON-Bioinformatics/covigator-ngs-pipeline: Release Covigator NGS pipeline v0.4.0
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)
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Additional details
Related works
- Is supplement to
- https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/tree/v0.4.0 (URL)