name	version	description	link
AMRFinder+	3.6.7	Find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences	https://github.com/ncbi/amr
Aragorn	1.2.38	Finds transfer RNA features (tRNA)	http://130.235.244.92/ARAGORN/Downloads/
Ariba	2.14.4	Antimicrobial Resistance Identification By Assembly	https://github.com/sanger-pathogens/ariba
ART	2016.06.05	A set of simulation tools to generate synthetic next-generation sequencing reads	https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm
assembly-scan	0.3.0	Generate basic stats for an assembly	https://github.com/rpetit3/assembly-scan
Barrnap	0.9	Bacterial ribosomal RNA predictor	https://github.com/tseemann/barrnap
BBMap	38.76	A suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.	https://jgi.doe.gov/data-and-tools/bbtools/
BCFtools	1.9	Utilities for variant calling and manipulating VCFs and BCFs.	https://github.com/samtools/bcftools
Bedtools	2.29.2	A powerful toolset for genome arithmetic.	https://github.com/arq5x/bedtools2
BioPython	1.76	Tools for biological computation written in Python	https://github.com/biopython/biopython
BLAST+	2.9.0	Basic Local Alignment Search Tool	https://blast.ncbi.nlm.nih.gov/Blast.cgi
Bowtie2	2.4.1	A fast and sensitive gapped read aligner	https://github.com/BenLangmead/bowtie2
BWA	0.7.17	Burrows-Wheeler Aligner for short-read alignment	https://github.com/lh3/bwa/
CD-HIT	4.8.1	Accelerated for clustering the next-generation sequencing data	https://github.com/weizhongli/cdhit
CheckM	1.1.2	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	https://github.com/Ecogenomics/CheckM
ClonalFrameML	1.12	Efficient Inference of Recombination in Whole Bacterial Genomes	https://github.com/xavierdidelot/ClonalFrameML
DiagrammeR	1.0.0	Graph and network visualization using tabular data in R 	https://github.com/rich-iannone/DiagrammeR
DIAMOND	0.9.35	Accelerated BLAST compatible local sequence aligner	https://github.com/bbuchfink/diamond
eggNOG-Mapper	2.0.1	Fast genome-wide functional annotation through orthology assignment	https://github.com/eggnogdb/eggnog-mapper
EMIRGE	0.61.1	Reconstructs full length ribosomal genes from short read sequencing data	https://github.com/csmiller/EMIRGE
FastANI	1.3	Fast Whole-Genome Similarity (ANI) Estimation	https://github.com/ParBLiSS/FastANI
FastTree 2	2.1.10	Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences	http://www.microbesonline.org/fasttree
fastq-dl	1.0.3	Download FASTQ files from SRA or ENA repositories	https://github.com/rpetit3/fastq-dl
FastQC	0.11.9	A quality control analysis tool for high throughput sequencing data.	https://github.com/s-andrews/FastQC
fastq-scan	0.4.3	Output FASTQ summary statistics in JSON format	https://github.com/rpetit3/fastq-scan
FLASH	1.2.11	A fast and accurate tool to merge paired-end reads	https://ccb.jhu.edu/software/FLASH/
freebayes	1.3.2	Bayesian haplotype-based genetic polymorphism discovery and genotyping	https://github.com/ekg/freebayes
GNU Parallel	20200122	A shell tool for executing jobs in parallel	https://www.gnu.org/software/parallel/
GTDB-tk	1.0.2	A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes	https://github.com/Ecogenomics/GTDBTk
HMMER	3.3	Biosequence analysis using profile hidden Markov models	http://hmmer.org/
Infernal	1.1.2	Searches DNA sequence databases for RNA structure and sequence similarities	http://eddylab.org/infernal/
IQ-TREE	1.6.12	Efficient phylogenomic software by maximum likelihood	https://github.com/Cibiv/IQ-TREE
ISMapper	2	IS mapping software	https://github.com/jhawkey/IS_mapper
Lighter	1.1.2	Fast and memory-efficient sequencing error corrector	https://github.com/mourisl/Lighter
MAFFT	7.455	Multiple alignment program for amino acid or nucleotide sequences	https://mafft.cbrc.jp/alignment/software/
Mash	2.2.2	Fast genome and metagenome distance estimation using MinHash	https://github.com/marbl/Mash
Mashtree	1.1.2	Create a tree using Mash distances	https://github.com/lskatz/mashtree
maskrc-svg	0.5	Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG	https://github.com/kwongj/maskrc-svg
McCortex	1	De novo genome assembly and multisample variant calling	https://github.com/mcveanlab/mccortex
MEGAHIT	1.2.9	Ultra-fast and memory-efficient (meta-)genome assembler	https://github.com/voutcn/megahit
MinCED	0.4.2	Mining CRISPRs in Environmental Datasets	https://github.com/ctSkennerton/minced
Minimap2	2.17	A versatile pairwise aligner for genomic and spliced nucleotide sequences	https://github.com/lh3/minimap2
ncbi-genome-download	0.2.12	Scripts to download genomes from the NCBI FTP servers	https://github.com/kblin/ncbi-genome-download
Nextflow	19.10.0	A DSL for data-driven computational pipelines	https://github.com/nextflow-io/nextflow
phyloFlash	3.3b3	Rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.	https://github.com/HRGV/phyloFlash
Pigz	2.3.4	A parallel implementation of gzip for modern multi-processor, multi-core machines	https://zlib.net/pigz/
Pilon	1.23	An automated genome assembly improvement and variant detection tool	https://github.com/broadinstitute/pilon/
PIRATE	1.0.3	A toolbox for pangenome analysis and threshold evaluation	https://github.com/SionBayliss/PIRATE
pplacer	1.1.alpha19	Phylogenetic placement and downstream analysis	https://github.com/matsen/pplacer
Prodigal	2.6.3	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	https://github.com/hyattpd/Prodigal
Prokka	1.4.5	Rapid prokaryotic genome annotation	https://github.com/tseemann/prokka
QUAST	5.0.2	Quality Assessment Tool for Genome Assemblies	http://quast.sourceforge.net/
Racon	1.4.13	Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads	https://github.com/lbcb-sci/racon
Roary	3.13.0	Rapid large-scale prokaryote pan genome analysis	https://github.com/sanger-pathogens/Roary
samclip	0.2	Filter SAM file for soft and hard clipped alignments	https://github.com/tseemann/samclip
SAMtools	1.9	Tools for manipulating next-generation sequencing data	https://github.com/samtools/samtools
Seqtk	1.3	A fast and lightweight tool for processing sequences in the FASTA or FASTQ format	https://github.com/lh3/seqtk
Shovill	1.0.9se	Faster assembly of Illumina reads	https://github.com/tseemann/shovill
SKESA	2.3.0	Strategic Kmer Extension for Scrupulous Assemblies	https://github.com/ncbi/SKESA
Snippy	4.4.5	Rapid haploid variant calling and core genome alignment	https://github.com/tseemann/snippy
SnpEff	4.3.1	Genomic variant annotations and functional effect prediction toolbox	http://snpeff.sourceforge.net/
snp-dists	0.6.3	Pairwise SNP distance matrix from a FASTA sequence alignment	https://github.com/tseemann/snp-dists
SNP-sites	2.5.1	Rapidly extracts SNPs from a multi-FASTA alignment	https://github.com/sanger-pathogens/snp-sites
Sourmash	3.2.0	Compute and compare MinHash signatures for DNA data sets	https://github.com/dib-lab/sourmash
SPAdes	3.13.0	An assembly toolkit containing various assembly pipelines	https://github.com/ablab/spades
Trimmomatic	0.39	A flexible read trimming tool for Illumina NGS data	http://www.usadellab.org/cms/index.php?page=trimmomatic
Unicycler	0.4.8	Hybrid assembly pipeline for bacterial genomes	https://github.com/rrwick/Unicycler
vcf-annotator	0.5	Add biological annotations to variants in a VCF file	https://github.com/rpetit3/vcf-annotator
Vcflib	1.0.0rc3	A simple C++ library for parsing and manipulating VCF files	https://github.com/vcflib/vcflib
Velvet	1.2.10	Short read de novo assembler using de Bruijn graphs	https://github.com/dzerbino/velvet
VSEARCH	2.14.1	Versatile open-source tool for metagenomics	https://github.com/torognes/vsearch
vt	2015.11.10	A tool set for short variant discovery in genetic sequence data	https://github.com/atks/vt
