xlavir 0.5.0

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

0.5.0 (2021-07-30)

• Added support for Nanopolish VCF parsing as generated by the ARTIC pipeline

• Added deduplication of VCF and SnpSift entries since the ARTIC pipeline may produce VCF files with duplicate variant calls due to overlap between amplicons.

• Added VCF and SnpSift test data for CLI test to generate Excel report.

0.4.3 (2021-07-29)

• Fix an issue where single base positions are being reported as 0-based when all other ranges are 1-based for reporting of low/no coverage regions from Mosdepth per-base BED files (#10).

0.4.2 (2021-05-21)

• Add support for nf-core/viralrecon version 2.0 (requires Mosdepth bed.gz files be output; needs custom modules.config like this one)

• Nextclade CLI per sample results parsed into sheet showing useful info like Nextstrain clade, # of mutations, # of PCR primer changes

• Added check that input directory exists and is a directory

• Added sheet with xlavir info

• Added Gene, Variant Effect, Variant Impact, Amino Acid Change to Variant Summary table

0.4.1 (2021-05-14)

• Add reference sequence length to QC stats table. Get ref seq length from max mosdepth per base BED coverage value.

• Add more conditional formatting

• Fix execution_report.html finding

• Fix version printing; add to help

• Add epilog with usage info

0.4.0 (2021-04-23)

• Adds “Variants Summary” sheet summarizing variant information across all samples

• Adds comments to AF values in “Variant Matrix” sheet

• Fixes width/height of cell comments to be based on length of comment text

0.3.0 (2021-04-23)

• Adds support for adding Ct values from a Ct values table (tab-delimited, CSV, ODS, XLSX format) into an xlavir report.

0.2.4 (2021-04-19)

• Fixes issue with SnpSift table file parsing and variable naming in variants.py (#4, #5)

0.2.3 (2021-04-19)

• Fixes issue with SnpSift table file parsing. Adds check to see if SnpSift column is dtype object/str before using .str Series methods (#4)

0.2.2 (2021-03-30)

• Fixes issue with SnpEff/SnpSift AA change parsing.

0.2.1 (2021-03-29)

• Fix division by zero error due to variants with DP values of 0

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)