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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. bactopia
    354 84,058
    A flexible pipeline for complete analysis of bacterial genomes

    bactopia nextflow bioconda

  2. dragonflye
    100 28,784
    Assemble bacterial isolate genomes from Nanopore reads

    dragonflye bioconda

  3. fastq-dl
    228 24,321
    Download FASTQ files from SRA or ENA repositories.

    fastq sra ena

  4. staphopia
    7 ?
    A workflow and database focused on the genomes of the bacterial pathogen Staphylococcus aureus

    staphopia nextflow

Software

  1. assembly-scan
    8 15,784
    Generate basic stats for an assembly

    summary fasta assembly

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

    variant vcf archived

  3. ena-dl
    0 2,464
    Download FASTQ files from ENA (archived)

    fastq ena archived

  4. fastq-scan
    27 30,150
    Output FASTQ summary statistics in JSON format

    summary fastq

  5. goblin
    2 932
    GOBLIN - Generate trusted prOteins to supplement BacteriaL annotatIoN

    prokka proteins bioconda

  6. illumina-cleanup
    3 4,246
    A Nextflow pipeline for pre-processing Illumina FASTQ files

    fastq qc nextflow

  7. illumina-simulation
    0 ?
    Dockerized Illumina sequencing simulation and 31-mer counting using ART and Jellyfish

    simulation illumina

  8. pasty
    11 4,123
    A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates

    pasty serotype bioconda

  9. pbptyper
    9 6,102
    In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies

    pbptyper serotype bioconda

  10. pmga
    0 3,196
    A fork of PMGA (PubMLST Genome Annotator) for all Neisseria species and Haemophilus influenzae

    pmga serotype bioconda

  11. shovill-se
    0 5,041
    A fork of Shovill that includes support for single end reads

    assembly single-end

  12. staphopia-sccmec
    0 2,540
    A standalone version of Staphopia’s SCCmec typing method.

    staphopia sccmec typing

  13. tbl2asn-forever
    2 61,255
    A fork of tbl2asn-forever available from Bioconda

    tbl2asn-forever prokka

  14. vcf-annotator
    24 11,515
    Add biological annotations to variants in a given VCF file.

    annotation vcf genbank variant