Dependencies

Warning

This documentation is for AMR++ version 2.0. Click here for the latest docs.

AmrPlusPlus uses a variety of open-source tools. The tools used, descriptions, and version specifics are provided below.

Bedtools

• 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

BWA

• 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

Kraken2

• 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

RarefactionAnalyzer

• 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

ResistomeAnalyzer

• 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

Samtools

• 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

SNPFinder

• 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

Trimmomatic

• 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

Freebayes

• 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

Resistance Gene Identifier

• 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