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    108 repositories

    • .github

      Public
      0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

    • binfie-notes

      Public
      Bioinformatics notes
      JavaScript
      •
      MIT License
      •1.6k•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • n50

      Public
      Calculate N50 from FASTA and FASTX files
      C
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • best-practices

      Public
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • datasciencegroup

      Public
      Scripts and docs from the datascienceatqib group
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Jan 30, 2025Jan 30, 2025

    • ARG-Sniper

      Public
      Benchmarking of AMR detection tools using shot-gun metagenomic datasets
      Python
      •
      Apache License 2.0
      •2•0•1•0•Updated Jan 29, 2025Jan 29, 2025

    • QuaTradis

      Public
      A pipeline to analyse transposon directed insertion-site sequencing
      Gnuplot
      •
      GNU General Public License v3.0
      •0•3•4•0•Updated Jan 23, 2025Jan 23, 2025

    • seqfu_v1

      Public
      Seqfu v1.x - Sequece Fastx Utilities
      Nim
      •
      GNU General Public License v3.0
      •8•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • sample-sheet-validator

      Public
      Svelte
      •
      MIT License
      •0•0•0•0•Updated Jan 18, 2025Jan 18, 2025

    • qimba

      Public
      Quadram Institute MetaBarcoding Analysis
      Python
      •
      MIT License
      •0•1•1•0•Updated Jan 17, 2025Jan 17, 2025

    • dadaist2

      Public
      Dadaist2 🟨 Highway to R
      bioinformaticstaxonomymetabarcoding16sphyloseqdada2asvamplicon-pipeline
      HTML
      •
      MIT License
      •5•13•1•0•Updated Jan 16, 2025Jan 16, 2025

    • nf-dehost

      Public
      Removing human sequences from short read samples using bowtie2
      Python
      •1•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • readfx

      Public
      SeqFu FASTX parser (klib)
      Nim
      •
      MIT License
      •3•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • cloudgene3

      Public
      A framework to build Software As A Service (SaaS) platforms for Nextflow pipelines.
      Java
      •
      MIT License
      •2•0•0•0•Updated Dec 14, 2024Dec 14, 2024

    • cg-irida

      Public
      Cloudgene yaml for https://github.com/quadram-institute-bioscience/nf-irida
      0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • nf-irida

      Public
      Simple NF workflow for preparing sample sheet of data from IRIDA
      Python
      •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • mc-spike

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • st_illumina_sample_sheet_validator

      Public
      Sample sheet validator for demultiplexing Illumina runs
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • sample_sheet_validator

      Public
      Python script validates the contents of a Nextseq 2k sample sheet, ensuring that it meets the expected format
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • qib-irida-uploader

      Public
      A wrapper of iridauploader for creating project and uploading samples to QIB IRIDA
      Python
      •1•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • ebame-viromics

      Public
      Ebame workshop website, built by P2PU
      SCSS
      •
      MIT License
      •504•0•0•0•Updated Oct 20, 2024Oct 20, 2024

    • phylobarcode

      Public
      <pilot> in-silico amplicons optimised for phylogenetic signal
      phylogeneticsmetabarcodingampliconprimers
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • mg-tk

      Public
      metagenomic toolkit - end-to-end solution for analysing metagenomes
      Perl
      •
      GNU General Public License v2.0
      •2•1•0•0•Updated Oct 9, 2024Oct 9, 2024

    • NBI-Slurm

      Public
      Experimental interface to slurm
      perl
      Perl
      •0•1•0•0•Updated Sep 25, 2024Sep 25, 2024

    • uvaia

      Public
      Reference-based alignment and sequence database search of SARS-CoV-2 genomes.
      genomicsnearest-neighbor-searchalignmentsearch-algorithmviral-genomicssars-cov-2bioinformatics
      C
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Sep 2, 2024Sep 2, 2024

    • peroba

      Public
      Phylogenetic Epidemiology with ROBust Assignment
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • biomcmc-lib

      Public
      C library with lowlevel functions used by other software
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • tatajuba

      Public
      Identification and classification of homopolymeric tracts from reads.
      genomicsphylogeneticsvariant-analysisbioinformatics
      C
      •
      GNU General Public License v3.0
      •0•5•2•0•Updated Aug 19, 2024Aug 19, 2024

    • amburana

      Public
      Alignment-free sequence clustering
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • biobakery-2024

      Public
      A QIB Workshop on popular tools part of the "BioBakery" suite (https://github.com/biobakery/biobakery)
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 13, 2024Aug 13, 2024