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    50 repositories

    • alndv

      Public
      call variants with deepvariant
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • alnsl

      Public
      Nextflow pipeline for short-read alignment
      nextflowmappingilluminamgishort-reads
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated May 22, 2025May 22, 2025

    • biomining_metagenomes

      Public
      Repository that holds data, scripts and figures regarding to the mining MAGs (Cauquenes tailing) article
      HTML
      •
      MIT License
      •1•1•0•0•Updated May 19, 2025May 19, 2025

    • snps_mags

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 2, 2025May 2, 2025

    • BRCA12_ms

      Public
      Code for figure and analysis of BRCA12 ms
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • ppilon

      Public
      Nextflow pipeline for polising a large genome using pilon
      Roff
      •
      MIT License
      •2•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • minibusco-nf

      Public
      Nextflow
      •0•0•0•0•Updated Apr 13, 2025Apr 13, 2025

    • hic-scaffolding-nf

      Public
      Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
      Nextflow
      •
      MIT License
      •5•0•0•0•Updated Apr 5, 2025Apr 5, 2025

    • Summer_Course_ML

      Public
      Material for the CMM summer course
      Jupyter Notebook
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • BRCA

      Public
      Nexflow pipeline for processing target BRCA data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • prok-annotate

      Public
      Annotation pipeline for prokaryotic genomes
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • nf-mag-depths

      Public
      A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins
      coveragebioinformaticsmetagenomicsshort-reads
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Jul 11, 2024Jul 11, 2024

    • somatic_point_mutations

      Public
      call somatic point mutations from tumor/normal pairs
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 21, 2024May 21, 2024

    • nf-gene-fusions

      Public
      A nextflow pipeline to call somatic gene fusions
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated May 20, 2024May 20, 2024

    • bam2cram

      Public
      A repository to convert BAM->CRAM files
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated May 1, 2024May 1, 2024

    • oncovirus

      Public
      prediction of somatic virus integration from WGS using hmftools
      MIT License
      •0•0•0•0•Updated Apr 1, 2024Apr 1, 2024

    • call_snv

      Public
      A nextflow pipeline to call SNV from short-read sequences
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jan 22, 2024Jan 22, 2024

    • nf-ngscheckmate

      Public
      Nextflow workflow running NGScheckmate
      Nextflow
      •1•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • nf-bakta

      Public
      A Nextflow pipeline for the annotation of bacterial genomes or MAGs running Bakta
      Nextflow
      •
      MIT License
      •1•1•1•0•Updated Oct 28, 2023Oct 28, 2023

    • nf-groot

      Public
      A Nextflow pipeline for running Groot: a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples.
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Sep 15, 2023Sep 15, 2023

    • prok-classify

      Public
      Assign objective taxonomic classifications to bacterial and archaeal genomes
      Nextflow
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 5, 2023Sep 5, 2023

    • 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
      •10•0•0•0•Updated Jul 27, 2023Jul 27, 2023

    • Germline-StructuralV-nf

      Public
      Germline structural variant calling pipeline for short read WGS datasets
      Nextflow
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Jul 13, 2023Jul 13, 2023

    • spg

      Public
      Simple Pan-Genome workflow for MAGs
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 9, 2023Jul 9, 2023

    • mag

      Public
      Assembly and binning of metagenomes
      Nextflow
      •
      MIT License
      •141•1•0•0•Updated Jun 8, 2023Jun 8, 2023

    • HBW

      Public
      Hybrid Binning Wengan (HBW)
      Makefile
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2023Jun 2, 2023

    • assemblyStats

      Public
      Run Assembly statistics on a genome assembly (BUSCO and assemblyStats and new_Assemblathon.pl)
      Perl
      •5•0•0•0•Updated Apr 28, 2023Apr 28, 2023

    • strelka2-nf

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Apr 14, 2023Apr 14, 2023

    • longreadstats

      Public
      Groovy
      •
      MIT License
      •1•0•0•0•Updated Mar 26, 2023Mar 26, 2023

    • purple-nf

      Public
      Nextflow pipeline for CNV calling with PURPLE
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Mar 18, 2023Mar 18, 2023