{
    "AMRFinder+": {
        "conda": {
            "name": "ncbi-amrfinderplus", 
            "yaml": "antimicrobial_resistance.yml"
        }, 
        "description": "Find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences", 
        "link": "https://github.com/ncbi/amr" 
    },
    "Aragorn": {
        "conda": {
            "name": "aragorn", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Finds transfer RNA features (tRNA)", 
        "link": "http://130.235.244.92/ARAGORN/Downloads/" 
    },
    "Ariba": {
        "conda": {
            "name": "ariba", 
            "yaml": "ariba_analysis.yml"
        }, 
        "description": "Antimicrobial Resistance Identification By Assembly", 
        "link": "https://github.com/sanger-pathogens/ariba" 
    },
    "ART": {
        "conda": {
            "name": "art", 
            "yaml": "gather_fastqs.yml"
        }, 
        "description": "A set of simulation tools to generate synthetic next-generation sequencing reads", 
        "link": "https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm" 
    },
    "assembly-scan": {
        "conda": {
            "name": "assembly-scan", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Generate basic stats for an assembly", 
        "link": "https://github.com/rpetit3/assembly-scan" 
    },
    "Barrnap": {
        "conda": {
            "name": "barrnap", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Bacterial ribosomal RNA predictor", 
        "link": "https://github.com/tseemann/barrnap" 
    },
    "BBMap": {
        "conda": {
            "name": "bbmap", 
            "yaml": "qc_reads.yml"
        }, 
        "description": "A suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data", 
        "link": "https://jgi.doe.gov/data-and-tools/bbtools/" 
    },
    "BCFtools": {
        "conda": {
            "name": "bcftools", 
            "yaml": "ariba_analysis.yml"
        }, 
        "description": "Utilities for variant calling and manipulating VCFs and BCFs", 
        "link": "https://github.com/samtools/bcftools" 
    },
    "Bedtools": {
        "conda": {
            "name": "bedtools", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "A powerful toolset for genome arithmetic", 
        "link": "https://github.com/arq5x/bedtools2" 
    },
    "BioPython": {
        "conda": {
            "name": "biopython", 
            "yaml": "ariba_analysis.yml"
        }, 
        "description": "Tools for biological computation written in Python", 
        "link": "https://github.com/biopython/biopython" 
    },
    "BLAST+": {
        "conda": {
            "name": "blast", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Basic Local Alignment Search Tool", 
        "link": "https://blast.ncbi.nlm.nih.gov/Blast.cgi" 
    },
    "Bowtie2": {
        "conda": {
            "name": "bowtie2", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "A fast and sensitive gapped read aligner", 
        "link": "https://github.com/BenLangmead/bowtie2" 
    },
    "BWA": {
        "conda": {
            "name": "bwa", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Burrows-Wheeler Aligner for short-read alignment", 
        "link": "https://github.com/lh3/bwa/" 
    },
    "CD-HIT": {
        "conda": {
            "name": "cd-hit", 
            "yaml": "ariba_analysis.yml"
        }, 
        "description": "Accelerated for clustering the next-generation sequencing data", 
        "link": "https://github.com/weizhongli/cdhit" 
    },
    "CheckM": {
        "conda": {
            "name": "checkm-genome", 
            "yaml": "assembly_qc.yml"
        }, 
        "description": "Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes", 
        "link": "https://github.com/Ecogenomics/CheckM" 
    },
    "ClonalFrameML": {
        "conda": {
            "name": "clonalframeml", 
            "yaml": "tools/roary/environment-linux.yml"
        }, 
        "description": "Efficient Inference of Recombination in Whole Bacterial Genomes", 
        "link": "https://github.com/xavierdidelot/ClonalFrameML" 
    },
    "DIAMOND": {
        "conda": {
            "name": "diamond", 
            "yaml": "tools/eggnog/environment-linux.yml"
        }, 
        "description": "Accelerated BLAST compatible local sequence aligner", 
        "link": "https://github.com/bbuchfink/diamond" 
    },
    "eggNOG-mapper": {
        "conda": {
            "name": "eggnog-mapper", 
            "yaml": "tools/eggnog/environment-linux.yml"
        }, 
        "description": "Fast genome-wide functional annotation through orthology assignment", 
        "link": "https://github.com/eggnogdb/eggnog-mapper" 
    },
    "FastANI": {
        "conda": {
            "name": "fastani", 
            "yaml": "tools/fastani/environment-linux.yml"
        }, 
        "description": "Fast Whole-Genome Similarity (ANI) Estimation", 
        "link": "https://github.com/ParBLiSS/FastANI" 
    },
    "FastTree 2": {
        "conda": {
            "name": "fasttree", 
            "yaml": "tools/gtdb/environment-linux.yml"
        }, 
        "description": "Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences", 
        "link": "http://www.microbesonline.org/fasttree" 
    },
    "fastq-dl": {
        "conda": {
            "name": "fastq-dl", 
            "yaml": "gather_fastqs.yml"
        }, 
        "description": "Download FASTQ files from SRA or ENA repositories", 
        "link": "https://github.com/rpetit3/fastq-dl" 
    },
    "FastQC": {
        "conda": {
            "name": "fastqc", 
            "yaml": "qc_reads.yml"
        }, 
        "description": "A quality control analysis tool for high throughput sequencing data", 
        "link": "https://github.com/s-andrews/FastQC" 
    },
    "fastq-scan": {
        "conda": {
            "name": "fastq-scan", 
            "yaml": "qc_reads.yml"
        }, 
        "description": "Output FASTQ summary statistics in JSON format", 
        "link": "https://github.com/rpetit3/fastq-scan" 
    },
    "FLASH": {
        "conda": {
            "name": "flash", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "A fast and accurate tool to merge paired-end reads", 
        "link": "https://ccb.jhu.edu/software/FLASH/" 
    },
    "freebayes": {
        "conda": {
            "name": "freebayes", 
            "yaml": "call_variants.yml"
        }, 
        "description": "Bayesian haplotype-based genetic polymorphism discovery and genotyping", 
        "link": "https://github.com/ekg/freebayes" 
    },
    "GNU Parallel": {
        "conda": {
            "name": "parallel", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "A shell tool for executing jobs in parallel", 
        "link": "https://www.gnu.org/software/parallel/" 
    },
    "GTDB-tk": {
        "conda": {
            "name": "gtdbtk", 
            "yaml": "tools/gtdb/environment-linux.yml"
        }, 
        "description": "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes", 
        "link": "https://github.com/Ecogenomics/GTDBTk" 
    },
    "HMMER": {
        "conda": {
            "name": "hmmer", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Biosequence analysis using profile hidden Markov models", 
        "link": "http://hmmer.org/" 
    },
    "Infernal": {
        "conda": {
            "name": "infernal", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Searches DNA sequence databases for RNA structure and sequence similarities", 
        "link": "http://eddylab.org/infernal/" 
    },
    "IQ-TREE": {
        "conda": {
            "name": "iqtree", 
            "yaml": "tools/phyloflash/environment-linux.yml"
        }, 
        "description": "Efficient phylogenomic software by maximum likelihood", 
        "link": "https://github.com/Cibiv/IQ-TREE" 
    },
    "ISMapper": {
        "conda": {
            "name": "ismapper", 
            "yaml": "tools/ismapper/environment-linux.yml"
        }, 
        "description": "IS mapping software", 
        "link": "https://github.com/jhawkey/IS_mapper" 
    },
    "Lighter": {
        "conda": {
            "name": "lighter", 
            "yaml": "qc_reads.yml"
        }, 
        "description": "Fast and memory-efficient sequencing error corrector", 
        "link": "https://github.com/mourisl/Lighter" 
    },
    "MAFFT": {
        "conda": {
            "name": "mafft", 
            "yaml": "tools/phyloflash/environment-linux.yml"
        }, 
        "description": "Multiple alignment program for amino acid or nucleotide sequences", 
        "link": "https://mafft.cbrc.jp/alignment/software/" 
    },
    "Mash": {
        "conda": {
            "name": "mash", 
            "yaml": "minmers.yml"
        }, 
        "description": "Fast genome and metagenome distance estimation using MinHash", 
        "link": "https://github.com/marbl/Mash" 
    },
    "Mashtree": {
        "conda": {
            "name": "mashtree", 
            "yaml": "tools/mashtree/environment-linux.yml"
        }, 
        "description": "Create a tree using Mash distances", 
        "link": "https://github.com/lskatz/mashtree" 
    },
    "maskrc-svg": {
        "conda": {
            "name": "maskrc-svg", 
            "yaml": "tools/roary/environment-linux.yml"
        }, 
        "description": "Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG", 
        "link": "https://github.com/kwongj/maskrc-svg" 
    },
    "McCortex": {
        "conda": {
            "name": "mccortex", 
            "yaml": "count_31mers.yml"
        }, 
        "description": "De novo genome assembly and multisample variant calling", 
        "link": "https://github.com/mcveanlab/mccortex" 
    },
    "MEGAHIT": {
        "conda": {
            "name": "megahit", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Ultra-fast and memory-efficient (meta-)genome assembler", 
        "link": "https://github.com/voutcn/megahit" 
    },
    "MinCED": {
        "conda": {
            "name": "minced", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Mining CRISPRs in Environmental Datasets", 
        "link": "https://github.com/ctSkennerton/minced" 
    },
    "Minimap2": {
        "conda": {
            "name": "minimap2", 
            "yaml": "call_variants.yml"
        }, 
        "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences", 
        "link": "https://github.com/lh3/minimap2" 
    },
    "ncbi-genome-download": {
        "conda": {
            "name": "ncbi-genome-download", 
            "yaml": "download_references.yml"
        }, 
        "description": "Scripts to download genomes from the NCBI FTP servers", 
        "link": "https://github.com/kblin/ncbi-genome-download" 
    },
    "phyloFlash": {
        "conda": {
            "name": "phyloflash", 
            "yaml": "tools/phyloflash/environment-linux.yml"
        }, 
        "description": "Rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset", 
        "link": "https://github.com/HRGV/phyloFlash" 
    },
    "Pigz": {
        "conda": {
            "name": "pigz", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "A parallel implementation of gzip for modern multi-processor, multi-core machines", 
        "link": "https://zlib.net/pigz/" 
    },
    "Pilon": {
        "conda": {
            "name": "pilon", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "An automated genome assembly improvement and variant detection tool", 
        "link": "https://github.com/broadinstitute/pilon/" 
    },
    "PIRATE": {
        "conda": {
            "name": "pirate", 
            "yaml": "tools/pirate/environment-linux.yml"
        }, 
        "description": "A toolbox for pangenome analysis and threshold evaluation", 
        "link": "http://github.com/SionBayliss/PIRATE" 
    },
    "pplacer": {
        "conda": {
            "name": "pplacer", 
            "yaml": "tools/gtdb/environment-linux.yml"
        }, 
        "description": "Phylogenetic placement and downstream analysis", 
        "link": "https://github.com/matsen/pplacer" 
    },
    "Prodigal": {
        "conda": {
            "name": "prodigal", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Fast, reliable protein-coding gene prediction for prokaryotic genomes", 
        "link": "https://github.com/hyattpd/Prodigal" 
    },
    "Prokka": {
        "conda": {
            "name": "prokka", 
            "yaml": "annotate_genome.yml"
        }, 
        "description": "Rapid prokaryotic genome annotation", 
        "link": "https://github.com/tseemann/prokka" 
    },
    "QUAST": {
        "conda": {
            "name": "quast", 
            "yaml": "assembly_qc.yml"
        }, 
        "description": "Quality Assessment Tool for Genome", 
        "link": "http://quast.sourceforge.net/" 
    },
    "Racon": {
        "conda": {
            "name": "racon", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads", 
        "link": "https://github.com/lbcb-sci/racon" 
    },
    "Roary": {
        "conda": {
            "name": "roary", 
            "yaml": "tools/roary/environment-linux.yml"
        }, 
        "description": "Rapid large-scale prokaryote pan genome analysis", 
        "link": "https://github.com/sanger-pathogens/Roary" 
    },
    "samclip": {
        "conda": {
            "name": "samclip", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Filter SAM file for soft and hard clipped alignments", 
        "link": "https://github.com/tseemann/samclip" 
    },
    "SAMtools": {
        "conda": {
            "name": "samtools", 
            "yaml": "ariba_analysis.yml"
        }, 
        "description": "Tools for manipulating next-generation sequencing data", 
        "link": "https://github.com/samtools/samtools" 
    },
    "Seqtk": {
        "conda": {
            "name": "seqtk", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "A fast and lightweight tool for processing sequences in the FASTA or FASTQ format", 
        "link": "https://github.com/lh3/seqtk" 
    },
    "Shovill": {
        "conda": {
            "name": "shovill-se", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Faster assembly of Illumina reads", 
        "link": "https://github.com/tseemann/shovill" 
    },
    "SKESA": {
        "conda": {
            "name": "skesa", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Strategic Kmer Extension for Scrupulous Assemblies", 
        "link": "https://github.com/ncbi/SKESA" 
    },
    "Snippy": {
        "conda": {
            "name": "snippy", 
            "yaml": "call_variants.yml"
        }, 
        "description": "Rapid haploid variant calling and core genome alignment", 
        "link": "https://github.com/tseemann/snippy" 
    },
    "SnpEff": {
        "conda": {
            "name": "snpeff", 
            "yaml": "call_variants.yml"
        }, 
        "description": "Genomic variant annotations and functional effect prediction toolbox", 
        "link": "http://snpeff.sourceforge.net/" 
    },
    "snp-dists": {
        "conda": {
            "name": "snp-dists", 
            "yaml": "tools/roary/environment-linux.yml"
        }, 
        "description": "Pairwise SNP distance matrix from a FASTA sequence alignment", 
        "link": "https://github.com/tseemann/snp-dists" 
    },
    "SNP-sites": {
        "conda": {
            "name": "snp-sites", 
            "yaml": "call_variants.yml"
        }, 
        "description": "Rapidly extracts SNPs from a multi-FASTA alignment", 
        "link": "https://github.com/sanger-pathogens/snp-sites" 
    },
    "Sourmash": {
        "conda": {
            "name": "sourmash", 
            "yaml": "minmers.yml"
        }, 
        "description": "Compute and compare MinHash signatures for DNA data sets", 
        "link": "https://github.com/dib-lab/sourmash" 
    },
    "SPAdes": {
        "conda": {
            "name": "spades", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "An assembly toolkit containing various assembly pipelines", 
        "link": "https://github.com/ablab/spades" 
    },
    "Trimmomatic": {
        "conda": {
            "name": "trimmomatic", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "A flexible read trimming tool for Illumina NGS data", 
        "link": "http://www.usadellab.org/cms/index.php?page=trimmomatic" 
    },
    "Unicycler": {
        "conda": {
            "name": "unicycler", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Hybrid assembly pipeline for bacterial genomes", 
        "link": "https://github.com/rrwick/Unicycler" 
    },
    "vcf-annotator": {
        "conda": {
            "name": "vcf-annotator", 
            "yaml": "call_variants.yml"
        }, 
        "description": "Add biological annotations to variants in a VCF file", 
        "link": "https://github.com/rpetit3/vcf-annotator" 
    },
    "Vcflib": {
        "conda": {
            "name": "vcflib", 
            "yaml": "call_variants.yml"
        }, 
        "description": "A simple C++ library for parsing and manipulating VCF files", 
        "link": "https://github.com/vcflib/vcflib" 
    },
    "Velvet": {
        "conda": {
            "name": "velvet", 
            "yaml": "assemble_genome.yml"
        }, 
        "description": "Short read de novo assembler using de Bruijn graphs", 
        "link": "https://github.com/dzerbino/velvet" 
    },
    "VSEARCH": {
        "conda": {
            "name": "vsearch", 
            "yaml": "tools/phyloflash/environment-linux.yml"
        }, 
        "description": "Versatile open-source tool for metagenomics", 
        "link": "https://github.com/torognes/vsearch" 
    },
    "vt": {
        "conda": {
            "name": "vt", 
            "yaml": "call_variants.yml"
        }, 
        "description": "A tool set for short variant discovery in genetic sequence data", 
        "link": "https://github.com/atks/vt" 
    }
}
