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    56 repositories

    • B-GUT-decontamination

      Public
      Python
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • meTAline

      Public
      A snakemake pipeline for metagenomics analysis, it facilitates an efficient workflow to preprocess short reads metagenomics data: from read trimming and filtering, through host read subtraction to taxonomic classification using both k-mer and gene marker-based approaches, and functional profiling of the samples.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 30, 2025Apr 30, 2025

    • ghost_transfers

      Public
      R
      •2•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • redundans

      Public
      Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
      pythonpipelinedocker-imagepolymorphicgapclosingfastascaffoldingassembled-contigsgenome-assembly
      C++
      •
      GNU General Public License v3.0
      •20•150•0•0•Updated Apr 14, 2025Apr 14, 2025

    • structural_phylome

      Public
      Compute a sequence and structure based phylome based on uniprot proteomes.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 24, 2025Mar 24, 2025

    • Q-PHAST

      Public
      Python
      •1•0•0•0•Updated Mar 19, 2025Mar 19, 2025

    • singularity-technical-seminar

      Public
      Technical seminar on containerizing bioinformatics pipelines 📦 🧬 💻 👩🏻‍💻 🧪
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 4, 2025Mar 4, 2025

    • perSVade

      Public
      perSVade: personalized Structural Variation detection
      Python
      •
      GNU General Public License v3.0
      •5•39•1•0•Updated Feb 26, 2025Feb 26, 2025

    • Cglabrata_tradeoffs

      Public
      Python
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • phylogenetic-reconstruction-for-hybrids

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • karyon

      Public
      This is the Karyon Pipeline
      Python
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Sep 13, 2024Sep 13, 2024

    • C_albicans_with_albumin

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

    • jloh

      Public
      A tool to extract LOH blocks from VCF, BAM and FASTA data
      heterozygositybioinformaticsgenomics
      Python
      •
      GNU General Public License v3.0
      •3•23•1•0•Updated Aug 30, 2024Aug 30, 2024

    • extract-kraken-output-reads

      Public
      Extracts reads classified by Kraken as a specified taxonomy ID. Those reads are extracted into a new FASTA file. This tool is direct refactored derivation from the [KrakenTools repository's extract_kraken_reads scripts](https://github.com/jenniferlu717/KrakenTools/blob/master/extract_kraken_reads.py)
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 13, 2024Aug 13, 2024

    • crosslink-by-sequence

      Public
      A tool to crosslink proteins between two proteomes from different sources using their sequences, aiming to avoid the inaccuracies associated with source-specific IDs.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • haplotypo

      Public
      This is the Haplotypo repository
      Python
      •
      GNU General Public License v3.0
      •6•20•1•0•Updated May 24, 2024May 24, 2024

    • lung_microbiome_16S

      Public
      R
      •0•0•0•0•Updated May 20, 2024May 20, 2024

    • ete

      Public
      Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
      Python
      •
      GNU General Public License v3.0
      •219•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • how2code

      Public
      Technical seminar regarding good practices in writing code and documentation
      Python
      •0•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • Candida_nextPARS

      Public
      Python
      •0•0•0•0•Updated Jan 29, 2024Jan 29, 2024

    • crossmapper

      Public
      Crossmapper software
      Python
      •
      GNU General Public License v3.0
      •1•9•3•0•Updated Dec 22, 2023Dec 22, 2023

    • last

      Public
      "Fork" of LAST (https://gitlab.com/mcfrith/last) v1418
      C++
      •1•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • hgt_detection

      Public
      Python
      •1•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • reconciler

      Public
      Python
      •1•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • phylomedb_speciestree

      Public
      Python
      •1•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • Candida_Selection_DrugResistance

      Public
      Python
      •2•4•0•0•Updated Sep 1, 2023Sep 1, 2023

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.5k•0•0•0•Updated Aug 28, 2023Aug 28, 2023

    • nextPARS

      Public
      Python
      •0•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • longHam

      Public
      LongHam assembly pipeline
      genomics
      Python
      •0•1•0•0•Updated Aug 4, 2023Aug 4, 2023

    • intermine

      Public
      Stable version of intermine used by candidamine and modified by us
      candidaminestable-version
      Java
      •
      Other
      •351•0•0•0•Updated May 21, 2023May 21, 2023