xlavir 0.2.0

Excel report from viral sequencing analysis output

xlavir

Excel report from viral sequencing data analysis output from the nf-core/viralrecon or peterk87/nf-virontus Nextflow pipelines.

• Free software: MIT license

• Documentation: https://xlavir.readthedocs.io.

Features

• Collect sample results from a nf-core/viralrecon or peterk87/nf-virontus into a Excel report

  • Samtools read mapping stats (flagstat)

  • Mosdepth read mapping coverage information

  • Variant calling information (SnpEff and SnpSift results, VCF file information)

  • Consensus sequences

• QA/QC of sample analysis results (basic PASS/FAIL based on minimum genome coverage and depth)

• Nextflow workflow execution information

• Prepend worksheets from other Excel documents into the report (e.g. cover page/sheet, sample sheet, lab results)

• Add custom images into worksheets with custom names and descriptions (e.g. phylogenetic tree figure PNG)

Roadmap

• Bcftools variant calling stats sheet

• Sample metadata table to merge with certain stats?

• YAML config to info sheet?

• coverage chart with controls?

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.2.0 (2021-03-04)

• Added header comments with descriptions of field content

• Added comment to Variant Matrix sheet A1 cell describing what is shown in the matrix

• Added highlighting of samples failing QC in other sheets

• Fixed image scaling by determining image size with imageio

• Added Medaka / Longshot VCF parsing

0.1.1 (2021-02-16)

• Collect sample results from a nf-core/viralrecon or peterk87/nf-virontus into a Excel report

  • Samtools read mapping stats (flagstat)

  • Mosdepth read mapping coverage information

  • Variant calling information (SnpEff and SnpSift results, VCF file information)

  • Consensus sequences

• iVar VCF parsing

• QA/QC of sample analysis results (basic PASS/FAIL based on minimum genome coverage and depth)

• Nextflow workflow execution information

• Prepend worksheets from other Excel documents into the report (e.g. cover page/sheet, sample sheet, lab results)

• Add custom images into worksheets with custom names and descriptions (e.g. phylogenetic tree figure PNG)