ggautreau

ggautreau's Stars

• steineggerlab/foldseek

  Foldseek enables fast and sensitive comparisons of large structure sets.

  Language:C83818339103

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R6041216165

• ComparativeGenomicsToolkit/cactus

  Official home of genome aligner based upon notion of Cactus graphs

  Language:C52822870111

• opencobra/cobrapy

  COBRApy is a package for constraint-based modeling of metabolic networks.

  Language:Python46737670218

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python4521423955

• pangenome/pggb

  the pangenome graph builder

  Language:Shell3961417444

• labgem/PPanGGOLiN

  Build a partitioned pangenome graph from microbial genomes

  Language:Python2421314530

• jiarong/VirSorter2

  customizable pipeline to identify viral sequences from (meta)genomic data

  Language:Python224421531

• lh3/gfatools

  Tools for manipulating sequence graphs in the GFA and rGFA formats

  Language:C214173321

• pmelsted/bifrost

  Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

  Language:C++206127225

• bluenote-1577/sylph

  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

  Language:Rust1913177

• cdanielmachado/carveme

  CarveMe: genome-scale metabolic model reconstruction

  Language:Python159819053

• uvemas/ViTables

  ViTables, a GUI for PyTables

  Language:Python15488455

• pirovc/genome_updater

  Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

  Language:Shell14614315

• eblerjana/pangenie

  Pangenome-based genome inference

  Language:C++11448110

• neherlab/pangraph

  A bioinformatic toolkit to align genome assemblies into pangenome graphs

  Language:Julia908237

• maickrau/MBG

  Language:C++574262

• AuReMe/metage2metabo

  From annotated genomes to metabolic screening in large scale microbiotas

  Language:Jupyter Notebook536507

• padlocbio/padloc

  Locate antiviral defence systems in prokaryotic genomes

  Language:R4844310

• rchikhi/2022-pangenome-graphs-intro

  Language:Python21205

• IFB-ElixirFr/EBAII

  Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"

  Language:HTML1326021

• CMU-SAFARI/SeGraM

  Source code for the software implementation of SeGraM proposed in our ISCA 2022 paper: Senol Cali et. al., "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping" at https://people.inf.ethz.ch/omutlu/pub/SeGraM_genomic-sequence-mapping-universal-accelerator_isca22.pdf

  Language:C12712

• danielriosgarza/MAMBO

  Language:Python123144

• metagenopolis/meteor

  Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform specie level taxonomic assignments and functional analysis.

  Language:Python124300

• metagenopolis/CroCoDeEL

  CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data

  Language:Python10200

• TimRouze/supersampler

  SuperSampler, an efficient scaled size sketching and sketch comparison tool

  Language:C++8301

• alenana99/memod

  Language:C320

• jpjarnoux/PanGraph-DB

  Artifact corresponding to the PanGraph-DB framework for performing complex multi-pangenome analyses using a graph database system.

  Language:Jupyter Notebook3300

• dubssieg/gfagraphs

  Library to parse, edit and handle in memory GFA graphs

  Language:Python2141

• D4GEN-Genopole/I-E-Pan

  Développement des outils informatiques pour l'analyse de données - Projet porté par Guillame GAUTREAU - INRAE

  Language:HTML1100