Repositories list

• B-GUT-decontamination

  Public
  Python

  •0•0•0•0•Updated Oct 9, 2025Oct 9, 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 Oct 2, 2025Oct 2, 2025

• perSVade

  Public
  perSVade: personalized Structural Variation detection

  Python

  •

  GNU General Public License v3.0

  •5•40•0•0•Updated Sep 9, 2025Sep 9, 2025

• brlens

  Public
  Python

  •0•0•0•0•Updated Jul 17, 2025Jul 17, 2025

• structural_phylome

  Public
  Compute a sequence and structure based phylome based on uniprot proteomes.

  Python

  •

  GNU General Public License v3.0

  •1•6•0•0•Updated Jul 8, 2025Jul 8, 2025

• crossmapper

  Public
  Crossmapper software

  Python

  •

  GNU General Public License v3.0

  •1•9•3•0•Updated Jun 13, 2025Jun 13, 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.

  pythonbioinformaticspipeline+ 14genomicsassemblydocker-imagepolymorphicgapclosingfasta+ 7

  C++

  •

  GNU General Public License v3.0

  •21•160•0•0•Updated Apr 14, 2025Apr 14, 2025

• Q-PHAST

  Public
  Python

  •2•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

• 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

  bioinformaticsgenomicsheterozygosity

  Python

  •

  GNU General Public License v3.0

  •4•25•1•3•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•22•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

  •222•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

• 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

  •3.6k•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