AmrPlusPlus uses a variety of open-source tools. The tools used, descriptions, and version specifics are provided below.
- Description: Bedtools is a suite of tools that can be used to compute and extract useful information from BAM, BED, and BCF files.
- Version: 2.28.0
- DOI: https://doi.org/10.1093/bioinformatics/btq033
- Description: BWA is a short and long read sequence aligner for aligning raw sequence data to a reference genome.
- Version: 0.7.17
- DOI: https://doi.org/10.1093/bioinformatics/btp324
- Description: Kraken is a fast taxonomic sequence classifier that assigns taxonomy labels to short-reads.
- Version: 2.0.8
- DOI: https://doi.org/10.1186/gb-2014-15-3-r46
- Description: RarefactionAnalyzer is a tool that can be used for performing rarefaction analysis.
- Version: 0.0.0
- DOI: https://doi.org/10.1093/nar/gkw1009
- Description: ResistomeAnalyzer is a tool for analyzing the resistome of large metagenomic datasets.
- Version: 0.0.0
- DOI: https://doi.org/10.1093/nar/gkw1009
- Description: Samtools is a program for manipulating and extracting useful information from alignment files in SAM or BAM format.
- Version: 1.9
- DOI: https://doi.org/10.1093/bioinformatics/btp352
- Description: SNPFinder is a haplotype variant caller that can be used for metagenomics datasets.
- Version: 0.0.0
- DOI: https://doi.org/10.1093/nar/gkw1009
- Description: Trimmomatic is a tool for removing low quality base pairs (bps) and adapter sequences from raw sequence data.
- Version: 0.39
- DOI: https://doi.org/10.1093/bioinformatics/btu170
- Description: Trimmomatic is a tool for removing low quality base pairs (bps) and adapter sequences from raw sequence data.
- Version: 1.3.1
- https://arxiv.org/abs/1207.3907v2
- Description: Trimmomatic is a tool for removing low quality base pairs (bps) and adapter sequences from raw sequence data.
- Version: 0.39
- https://card.mcmaster.ca/analyze/rgi