Repositories list

• fluflo

  Public
  Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

  nextflowphylogeneticstrees+ 3nextstrainauspicemicrobes

  Nextflow

  •

  GNU General Public License v3.0

  •4•8•0•0•Updated Feb 1, 2025Feb 1, 2025

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •162•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• fluviewer-nf

  Public
  Nextflow pipeline for influenza A whole genome sequence analysis

  Nextflow

  •1•0•8•5•Updated Jan 30, 2025Jan 30, 2025

• WasteFlow

  Public
  Nextflow pipeline for pathogen surveillance in wastewater

  nextflowsurveillancewastewater+ 3freyjasars-cov-2microbes

  Nextflow

  •

  GNU General Public License v3.0

  •1•5•0•0•Updated Jan 27, 2025Jan 27, 2025

• auspice-docker

  Public
  Dockerfile

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• alignment-variants

  Public
  Pipeline to perform alignment & variant calling on whole-genome sequence data

  microbial-genomicsvariant-callingread-mapping

  Python

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• routine-nanopore-qc-collector

  Public
  Collect Routine QC for Nanopore Sequence Data

  quality-controlmicrobial-genomicsdata-management

  Python

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• auto-routine-nanopore-qc

  Public
  Python

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• simulate-long-reads

  Public
  Generate simulated oxford nanopore reads from a reference sequence

  next-generation-sequencingdata-simulationmicrobial-genomics

  Nextflow

  •1•4•0•0•Updated Jan 22, 2025Jan 22, 2025

• downsample-reads

  Public
  Downsample fastq reads for mutiple samples, at multiple depths

  Nextflow

  •1•0•2•0•Updated Jan 16, 2025Jan 16, 2025

• basic-sequence-qc

  Public
  Generate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.

  quality-controlgenomicsnext-generation-sequencing+ 1bioinformatics-pipeline

  Python

  •

  MIT License

  •0•1•1•0•Updated Dec 18, 2024Dec 18, 2024

• snippy-core-phylogenomics

  Public
  Nextflow

  •2•1•4•1•Updated Dec 5, 2024Dec 5, 2024

• tbprofiler-nf

  Public
  Nextflow Wrapper for TBProfiler

  bioinformatics-pipelinemicrobial-genomicstuberculosis-classification

  Python

  •2•4•4•1•Updated Dec 4, 2024Dec 4, 2024

• taxon-abundance

  Public
  Python

  •1•5•7•0•Updated Dec 4, 2024Dec 4, 2024

• plasmid-assembly

  Public
  Nextflow

  •

  MIT License

  •0•0•3•0•Updated Nov 8, 2024Nov 8, 2024

• snippy-variants

  Public
  Perform read mapping and variant calling using snippy

  microbial-genomicsvariant-calling

  Nextflow

  •1•0•4•3•Updated Nov 4, 2024Nov 4, 2024

• mpxv-artic-nf

  Public
  Nextflow

  •4•2•1•0•Updated Oct 30, 2024Oct 30, 2024

• process-nanopore

  Public
  A pipeline for processing raw sequence data from nanopore runs

  Python

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• norovirus-blast-nf

  Public
  nextflow wrapper for noroblast

  Nextflow

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• amplicone

  Public
  Python

  •

  MIT License

  •1•0•1•0•Updated Oct 11, 2024Oct 11, 2024

• cpo-results-collector

  Public
  Python

  •0•0•3•0•Updated Oct 8, 2024Oct 8, 2024

• amplicon-consensus

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• artic-mpxv2022

  Public
  0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

• auto-ncov

  Public
  Automated genomic analysis of SARS-CoV-2 sequence data

  automationmicrobial-genomicsgenomic-epidemiology

  Python

  •0•1•3•0•Updated Aug 30, 2024Aug 30, 2024

• nextclade-nf

  Public
  Pipeline for running nextclade

  Nextflow

  •0•0•0•0•Updated Aug 14, 2024Aug 14, 2024

• demultiplex-nanopore

  Public
  Demultiplex nanopore reads and combine into a single file per sample

  microbial-genomicsnanopore-sequencing

  Nextflow

  •0•1•0•0•Updated Jul 31, 2024Jul 31, 2024

• auto-cpo

  Public
  Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)

  automationmicrobial-genomics

  Python

  •

  GNU General Public License v3.0

  •0•0•5•0•Updated Jul 30, 2024Jul 30, 2024

• dehost-and-verify-illumina

  Public
  Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken

  quality-controlmicrobial-genomics

  Nextflow

  •0•1•3•0•Updated Jul 23, 2024Jul 23, 2024

• symlink-seqs

  Public
  Create fastq symlinks for selected samples in sequencer output directories based on several criteria

  next-generation-sequencingdata-managementillumina-sequencing+ 1symlinks-manager

  Python

  •0•0•2•0•Updated Jul 23, 2024Jul 23, 2024

• kma-cgmlst

  Public
  A cgMLST pipeline based on the KMA aligner

  bioinformatics-pipelinemicrobial-genomicscgmlst

  Nextflow

  •

  MIT License

  •2•4•3•0•Updated Jul 22, 2024Jul 22, 2024