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Dependencies

AMR++ uses a variety of open-source tools. The tools used, descriptions, and version specifics are provided below. These dependencies can be installed manually to your local computing cluster, or by changing the -profile parameter, they can be handled using conda, sigularity, or docker.

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

FastQC

  • Description: A quality control tool for high throughput sequence data.
  • Version: 0.11.8

multiQC

  • Description: Create aggregate bioinformatics analysis reports across many samples and tools
  • Version: 1.6
  • DOI: https://doi.org/10.1093/bioinformatics/btw354

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

AmrPlusPlus_SNP

  • Description: The AMRPlusPlus_SNP repository contains multiple progams used to either extract SNP info or to verify ARGs for resistant-conferring SNPs.
  • Version: 0.0.0
  • DOI:

Optional software

Bracken

  • Description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
  • Version: 2.7
  • DOI: 10.7717/peerj-cs.104

Krona

  • Description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
  • Version: 2.8.1
  • DOI: https://doi.org/10.1186/1471-2105-12-385