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    14 repositories

    • dryad

      Public
      Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.
      Groovy
      •
      GNU General Public License v3.0
      •6•17•1•1•Updated Feb 20, 2025Feb 20, 2025

    • SPNtypeID

      Public
      SPNtypeID is a Nextflow pipeline used for genome assembly and serotyping of Streptococcus pneumoniae.
      Nextflow
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Feb 13, 2025Feb 13, 2025

    • viralrecon

      Public
      Assembly and intrahost/low-frequency variant calling for viral samples
      Nextflow
      •
      MIT License
      •116•0•0•0•Updated Feb 13, 2025Feb 13, 2025

    • spriggan

      Public
      Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
      Python
      •
      GNU General Public License v3.0
      •3•15•0•0•Updated Feb 7, 2025Feb 7, 2025

    • seqCheck

      Public
      A simple and quick pipeline to check read quality and perform subsampling.
      Nextflow
      •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • miscellaneous_scripts

      Public
      This repository contains miscellaneous scripts for processing or analyzing bioinformatics data
      Python
      •0•0•0•1•Updated Dec 17, 2024Dec 17, 2024

    • aws-infra-nextflow

      Public
      HCL
      •
      GNU General Public License v3.0
      •0•9•0•0•Updated Nov 18, 2024Nov 18, 2024

    • nf-core-awsomicstest

      Public
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Nov 11, 2024Nov 11, 2024

    • mycosnp-nf

      Public
      CDCgov/mycosnp-nf
      Nextflow
      •
      Apache License 2.0
      •39•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • ar_report_generator

      Public
      AR Report Generator is used to render a report from the output of pipelines that identify antibiotic resistance (AR) genes and/or examine prokaryote relatedness in outbreaks
      Dockerfile
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Jan 2, 2024Jan 2, 2024

    • tbQC

      Public
      Groovy
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • amazon-ebs-autoscale

      Public
      Don't run out of disk space on your EC2 instance when generating or working with large files. Automatically add EBS volumes to a filesystem mount point in response to disk utilization.
      Shell
      •
      MIT License
      •61•0•0•0•Updated Feb 7, 2023Feb 7, 2023

    • docker_builds

      Public
      Dockerfile
      •0•0•0•0•Updated Jan 27, 2023Jan 27, 2023

    • augur-nf

      Public
      Nextflow implementation of Nextstrain's Augur pipeline
      Nextflow
      •3•1•1•0•Updated Dec 19, 2022Dec 19, 2022