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Fischbach Lab

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  1. ninjaMap ninjaMap Public

    Compute strain abundance in a defined microbial community

    Python 10 2

  2. nf-ninjamap nf-ninjamap Public

    ninjamap pipeline in nextflow

    Python 7 2

  3. nf-reads-profiler nf-reads-profiler Public

    Nextflow pipeline to run Metaphlan3 and Humann3 on QC-ed reads.

    Nextflow 4 1

  4. nf-blast nf-blast Public

    Blast tools using Nextflow on AWS Batch using database on a shared file system.

    Nextflow 1

  5. nf-hybridassembly nf-hybridassembly Public

    Hybrid assembly pipeline in nextflow

    Shell 1

  6. nf-cctyper nf-cctyper Public

    Nextflow 1

Repositories

Showing 10 of 34 repositories
  • nf-reads-profiler Public

    Nextflow pipeline to run Metaphlan3 and Humann3 on QC-ed reads.

    FischbachLab/nf-reads-profiler’s past year of commit activity
    Nextflow 4 GPL-3.0 1 0 0 Updated Jan 15, 2026
  • nf-ninjamap Public

    ninjamap pipeline in nextflow

    FischbachLab/nf-ninjamap’s past year of commit activity
    Python 7 GPL-3.0 2 0 0 Updated Jan 14, 2026
  • nf-megahit Public

    MAG assembly and binning

    FischbachLab/nf-megahit’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Oct 23, 2025
  • nf-ninjaindex Public

    Nextflow pipeline to build the ninja index for ninjaMap

    FischbachLab/nf-ninjaindex’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Oct 2, 2025
  • nf-binqc Public

    Bin QC

    FischbachLab/nf-binqc’s past year of commit activity
    Nextflow 0 GPL-3.0 0 0 0 Updated Jul 16, 2025
  • nf-dsqc Public

    Drug Substance QC pipeline

    FischbachLab/nf-dsqc’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Jun 12, 2025
  • nf-blast Public

    Blast tools using Nextflow on AWS Batch using database on a shared file system.

    FischbachLab/nf-blast’s past year of commit activity
    Nextflow 1 GPL-3.0 0 0 0 Updated Jun 6, 2025
  • nf-miseq-16s-dada2 Public

    MiSeq 16S DADA2 pipeline in nextflow

    FischbachLab/nf-miseq-16s-dada2’s past year of commit activity
    R 0 GPL-3.0 0 0 0 Updated Mar 26, 2025
  • nf-amr Public

    Run basic AMRFinderPlus on a set of genomes

    FischbachLab/nf-amr’s past year of commit activity
    Nextflow 0 GPL-3.0 0 0 0 Updated Mar 12, 2025
  • nf-hybridassembly Public

    Hybrid assembly pipeline in nextflow

    FischbachLab/nf-hybridassembly’s past year of commit activity
    Shell 1 GPL-3.0 0 0 0 Updated Feb 3, 2025
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