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    35 repositories

    • nf-ninjamap

      Public
      ninjamap pipeline in nextflow
      Python
      •
      GNU General Public License v3.0
      •2•7•0•0•Updated Jul 3, 2026Jul 3, 2026

    • nf-binqc

      Public
      Bin QC
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 24, 2026May 24, 2026

    • nf-transfer

      Public
      AWS S3 Cross-Account Transfer
      Nextflow
      •0•0•0•0•Updated May 13, 2026May 13, 2026

    • nf-miseq-16s-dada2

      Public
      MiSeq 16S DADA2 pipeline in nextflow
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • nf-megahit

      Public
      MAG assembly and binning
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • nf-reads-profiler

      Public
      Nextflow pipeline to run Metaphlan3 and Humann3 on QC-ed reads.
      Nextflow
      •
      GNU General Public License v3.0
      •3•4•0•0•Updated Jan 15, 2026Jan 15, 2026

    • nf-ninjaindex

      Public
      Nextflow pipeline to build the ninja index for ninjaMap
      Python
      •
      MIT License
      •0•0•1•0•Updated Oct 2, 2025Oct 2, 2025

    • nf-dsqc

      Public
      Drug Substance QC pipeline
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • nf-blast

      Public
      Blast tools using Nextflow on AWS Batch using database on a shared file system.
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 6, 2025Jun 6, 2025

    • nf-amr

      Public
      Run basic AMRFinderPlus on a set of genomes
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • nf-hybridassembly

      Public
      Hybrid assembly pipeline in nextflow
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 3, 2025Feb 3, 2025

    • nf-Sanger

      Public
      Sanger assembly and annotation pipeline
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • nf-bakta

      Public
      Use Bakta for speedy and consistent genome annotation
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • nf-eggnog

      Public
      Nextflow
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • nf-readqc

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • nf-basespace

      Public
      Nextflow
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • nf-phylogenetic-tree

      Public
      Build a phylogenetic tree from the full length 16S sequences
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • pub_djenet_sepi

      Public
      Discovery and engineering of the antibody response against a prominent skin commensal
      Roff
      •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •108•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • nf-maaslin2

      Public
      maaslin2
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • nf-spades

      Public
      A short-read assembly pipeline
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • nf-midas

      Public
      Nextflow
      •0•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • nf-cctyper

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 26, 2024Apr 26, 2024

    • nf-coptr

      Public
      CoPTR is a tool for estimating peak-to-trough ratios from metagenomic sequencing.
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 16, 2023Nov 16, 2023

    • ninjaMap

      Public
      Compute strain abundance in a defined microbial community
      Python
      •2•10•0•0•Updated Jul 27, 2023Jul 27, 2023

    • miti_small

      Public
      A catch all repo for all small MITI analysis projects.
      Jupyter Notebook
      •1•0•0•0•Updated Jul 13, 2023Jul 13, 2023

    • nf-nano-ninjamap

      Public
      Testing ONT long reads for ninjaMap
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 22, 2023May 22, 2023

    • nf-bacannot

      Public
      Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
      Nextflow
      •
      GNU General Public License v3.0
      •13•0•1•0•Updated May 18, 2023May 18, 2023

    • nagashima_etal_sbp

      Public
      Code for analysis and figures in Kazuki's paper
      Jupyter Notebook
      •0•0•0•0•Updated Dec 16, 2022Dec 16, 2022

    • sangeria

      Public
      Scripts related to Sanger assembly efforts
      Shell
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022
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