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    104 repositories

    • datasciencegroup

      Public
      Scripts and docs from the datascienceatqib group
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Jan 26, 2025Jan 26, 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

    • sample-sheet-validator

      Public
      Svelte
      •
      MIT License
      •0•0•0•0•Updated Jan 18, 2025Jan 18, 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 17, 2025Jan 17, 2025

    • qimba

      Public
      Quadram Institute MetaBarcoding Analysis
      Python
      •
      MIT License
      •0•0•0•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

    • readfx

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

    • binfie-notes

      Public
      Bioinformatics notes
      JavaScript
      •
      MIT License
      •1.6k•0•0•0•Updated Dec 29, 2024Dec 29, 2024

    • 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

    • n50

      Public
      Calculate N50 from FASTA and FASTX files
      C
      •
      MIT License
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 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
      •502•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

    • tweety-gut

      Public
      Metagenomic investigation of the faecal microbiomes of great tits and blue tits provides insights into the host, diet, pathogens and microbial biodiversity
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • 2024-campymags

      Public
      Datasets and scripts for article "Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • qib-jira

      Public
      Fetching records from QIB Cloud Jira to a local database
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • uflow

      Public
      USEARCH based workflow
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 8, 2024Jul 8, 2024