ViroMatch relies on third-party bioinformatics tools at various points in the pipeline. The table below lists the major third-party tools and how they are used.
| Software | Version | License | Link | ViroMatch Usage |
|---|---|---|---|---|
| BWA | 0.7.17-r1198-dirty | GNU General Public License version 3.0 (GPLv3), MIT License | http://bio-bwa.sourceforge.net/ | Used for nucleotide alignments. |
| Biopython | 1.78 | Biopython License Agreement | https://biopython.org/ | Used for FASTA/FASTQ handling. |
| Diamond | diamond v0.9.29.130 | GPL-3.0 License | http://www.diamondsearch.org/ | Used for translated nucleotide alignments. |
| Pandas | 1.1.2 | BSD-licensed library | https://pandas.pydata.org/ | Pandas used for data handling and reporting. |
| Python | Python 3.7.5 | Python License Agreement (GPL-compatible) | https://www.python.org/ | ViroMatch is written in Python. |
| Samtools | samtools 1.9 | The MIT License | http://www.htslib.org/ | Samtools is used for SAM/BAM handling. |
| Snakemake | 5.25.0 | The MIT License | https://snakemake.readthedocs.io/ | Snakemake is used for pipeline organization and execution. |
| fqtrim | v0.9.7 | Artistic License 2.0 | https://ccb.jhu.edu/software/fqtrim/ | Used for adaptor and quality trimming; also, short read filtering. |
| seqtk | 1.3-r115-dirty | The MIT License | https://github.com/lh3/seqtk | The seqtk package is used to extract specific reads from FASTQ files. |
| vsearch | v2.15.0_linux_x86_64 | GNU General Public License version 3 or BSD 2-clause license (dual-licensed) | https://github.com/torognes/vsearch | The vsearch package is used for low-complexity read masking/filtering. |