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VirSieve Aligner

Summary

This container is part of the Environmental Viral Detection pipeline and covers the pre-processing of raw reads and alignment as well as some post-alignment BAM file organization steps. This portion of the pipeline centers around Sickle and Scythe for trimming adapter contamination and bad quality sequence as well as BWA in MEM mode for alignment of short reads to the viral reference genome. The output of this pipeline will be merged BAM files aligned from the supplied raw reads.

SECURITY CONCERN: This pipeline is currently using os.system to run commands and sanitization was causing runs to fail. If running files from untrusted sources, please be sure to sanitize file names to prevent potential command injections into the container.

File naming and structure

The simplest way to run this pipeline is to set up a working directory where all of the subsequent files and folders will be created. In this folder, create a folder called rawFASTQ where you can put your paired and unpaired raw reads. File naming should follow the standard Illumina scheme where they will look something like this: sample-name_S6_L001_R1_001.fastq.gz. Please avoid the use of dots and underscores in your sample names, as those characters are used to identify the created files during processing. FASTQ files should all end with .fastq or .fq unless gzip compressed in which case they should end with fastq.gz or fq.gz. For adapter trimming to take place, include a FASTA-formatted file named adapters.fa in the rawFASTQ folder.

Running the container

To run this container (presumed to be named virsievealign here), simply use the following command:

docker container run --rm -v /path/to/working/folder:/data virsievealign

Setting non-default options

Some options can be set to non-default values by passing them into the container as environmental variables using the standard Docker commandline technique for setting environmental variables as follows:

Variable Type Default Description
WORKINGFOLDER string /data Working folder name within the container
INPUTFOLDER string /$WORKINGFOLDER/rawFASTQ The name of the raw sequence folder within the working folder
ADAPTERS string /$WORKINGFOLDER/$INPUTFOLDER/adapters.fa The fasta file with the adapter sequences for trimming
PROCESSEDREADFOLDER string /$WORKINGFOLDER/processedFASTQ The name of the folder for processed, unaligned reads
RAWBAMFOLDER string /$WORKINGFOLDER/rawBAM The name of the folder for the initial alignment files
MERGEDBAMFOLDER string /$WORKINGFOLDER/mergedBAM The name of the folder for the processed alignment files
REFGENOME string /home/biodocker/references/Sars_cov_2.ASM985889v3.dna_sm.toplevel.fa.gz Path to the BWA-indexed reference genome (the default reference genome is indexed on container build for efficiency)

Contributing

We welcome and encourage contributions to this project from the microbiomics community and will happily accept and acknowledge input (and possibly provide some free kits as a thank you). We aim to provide a positive and inclusive environment for contributors that is free of any harassment or excessively harsh criticism. Our Golden Rule: Treat others as you would like to be treated.

Versioning

We use a modification of Semantic Versioning to identify our releases.

Release identifiers will be major.minor.patch

Major release: Newly required parameter or other change that is not entirely backwards compatible Minor release: New optional parameter Patch release: No changes to parameters

Authors

See also the list of contributors who participated in this project.

License

This project is licensed under the GNU GPLv3 License - see the LICENSE file for details. This license restricts the usage of this application for non-open sourced systems. Please contact the authors for questions related to relicensing of this software in non-open sourced systems.

Acknowledgments

We would like to thank the following, without whom this would not have happened:

  • The Python Foundation
  • The staff at Zymo Research
  • The scientific and public health COVID response community
  • Our customers

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Alignment and related functionality for the VirSieve Pipeline by Zymo Research

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