wgscovplot 0.3.0

Generate interactive comparative sequencing coverage plots in self-contained, offline-friendly HTML files with optional annotation of variant calling results, PCR amplicon coverage and genetic features

wgscovplot

wgscovplot generates interactive comparative sequencing coverage plots in self-contained, offline-friendly HTML files with optional annotation of variant calling results, PCR amplicon coverage and genetic features.

• Live example output

Installation

From PyPI

Install from PyPI with pip

pip install wgscovplot

If the installation was successful, you should be able to type wgscovplot --help and get a help message on how to use the tool.

Install from source

Clone the wgscovplot repository.

git clone https://github.com/nhhaidee/wgscovplot.git

Then change directory to wgscovplot and install.

cd wgscovplot
python setup.py install

Features

• Compare sequencing coverage across multiple samples
• Fully-interactive plots with informative tooltips highlighting variant calling results and coverage statistics across all samples being shown
• Easy-to-use: Simply provide a nf-core/viralrecon, peterk87/nf-virontus, CFIA-NCFAD/nf-flu Nextflow workflow results directory as input (wgscovplot --input-dir /path/to/viralrecon/results) and wgscovplot will figure out what files it needs to generate its interactive sequencing coverage plots
• Annotate coverage plots with variant calling results from multiple different variant callers (iVar, Nanopolish, Longshot, Medaka) and variant effect results from SnpEff/SnpSift

Usage

Basic usage will output a wgscovplot.html file in the current directory:

wgscovplot --input-dir /path/to/viralrecon/results

Specify an NCBI Accession ID

wgscovplot \
  --input-dir /path/to/viralrecon/results \
  --ncbi-accession-id MN908947.3

Show help info with $ wgscovplot --help:

Usage: wgscovplot [OPTIONS]

Options:
  --input-dir PATH                Nextflow workflow results directory
                                  [required]
  --output-html PATH              Output File of Interactive HTML Coverage
                                  Plot  [default: wgscovplot.html]
  --ref-seq PATH                  Path to reference sequences
  --genbank PATH                  Genbank file contains gene features
  --ncbi-accession-id TEXT        NCBI accession id to fetch gene features
                                  and/or reference sequences
  --low-coverage-threshold INTEGER
                                  Low Coverage Threshold  [default: 10]
  --amplicon / --no-amplicon      Plot Amplicon Coverage Depth  [default:
                                  amplicon]
  --gene-feature / --no-gene-feature
                                  Plot Gene Features  [default: gene-feature]
  --segment-virus / --no-segment-virus
                                  Generate Coverage plot for segments virus
                                  [default: no-segment-virus]
  --gene-misc-feature / --no-gene-misc-feature
                                  Plot Miscellaneous Features  [default: no-
                                  gene-misc-feature]
  --dev / --no-dev                Run tool with debug mode  [default: no-dev]
  --verbose / --no-verbose        Verbose logs  [default: no-verbose]
  --version / --no-version        Print wgscovplot version and exit
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.
  --help                          Show this message and exit.

Dependencies

• Python (>=3.8)
  • BioPython
  • rich
  • typer
  • Pandas
  • requests
  • jinja2
• Javascript
  • npm or yarn for building JS bundle
  • Echarts for generating interactive plots
  • select2 for nice select boxes
  • Bootstrap for styling

Authors

• Development Lead: Peter Kruczkiewicz
• Software Developer: Hai Nguyen

License

Copyright 2021 Canadian Food Inspection Agency of Canada, Government of Canada.

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

History

0.3.0 (2022-08-31)

• Add support for segment virus (AIV)
• Accept result folder generated by nf-flu with option --segment-virus
• Annotate primer sequences with option --primer-seq. The primer sequence in fasta file

0.2.1 (2022-06-14)

• Fixed issues of tooltips displayed incorrectly due to samples list being reversed

0.2.0 (2022-03-28)

• Automatically Gene Bank and reference retrieval
• Automatically detect amplicon data and option to toggle amplicon bar
• Variant heat map is updated according to selected samples
• Downgrade and use Echarts v5.2.2 to fix the problem of amplicon plot (https://github.com/nhhaidee/wgscovplot/issues/36)
• Clean up code.

0.1.1 (2022-03-18)

Fixes parsing of Medaka VCF with low/no coverage variants.

0.1.0 (2022-03-04)

Initial alpha release.