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SOFTWARE.md

These are tools which I’ve put together over the years. With the execption to Staphopia (v2 is in the works!) all my tools are available on Bioconda. Currently, most of my effort is going towards Bactopia. So, if you try Bactopia, I would love to get any feedback you might have!

But that goes for the others too! If you use any of my tools and have feedback or run into a bug, please create an issue on their respective GitHub repository. I will try my best to help in any way that I can!

Pinned

  1. 187 32,046
    A flexible pipeline for complete analysis of bacterial genomes

    bactopia nextflow bioconda

  2. A workflow and database focused on the genomes of the bacterial pathogen Staphylococcus aureus

    staphopia nextflow

Software

  1. Generate basic stats for an assembly

    summary fasta assembly

  2. A ruffus pipeline to call variants following GATK best practices. (archived)

    variant vcf archived

  3. 50 7,618
    Assemble bacterial isolate genomes from Nanopore reads

    dragonflye bioconda

  4. 0 1,085
    Download FASTQ files from ENA (archived)

    fastq ena archived

  5. 46 7,357
    Download FASTQ files from SRA or ENA repositories.

    fastq sra ena

  6. 24 16,876
    Output FASTQ summary statistics in JSON format

    summary fastq

  7. A Nextflow pipeline for pre-processing Illumina FASTQ files

    fastq qc nextflow

  8. Dockerized Illumina sequencing simulation and 31-mer counting using ART and Jellyfish

    simulation illumina

  9. 3 115
    A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates

    pasty serotype bioconda

  10. In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies

    pbptyper serotype bioconda

  11. 0 885
    A fork of PMGA (PubMLST Genome Annotator) for all Neisseria species and Haemophilus influenzae

    pmga serotype bioconda

  12. 0 2,324
    A fork of Shovill that includes support for single end reads

    assembly single-end

  13. A standalone version of Staphopia’s SCCmec typing method.

    staphopia sccmec typing

  14. A fork of tbl2asn-forever available from Bioconda

    tbl2asn-forever prokka

  15. Add biological annotations to variants in a given VCF file.

    annotation vcf genbank variant