Pipelines used in the lab.
☆15Mar 26, 2025Updated 11 months ago
Alternatives and similar repositories for pipelines
Users that are interested in pipelines are comparing it to the libraries listed below
Sorting:
- the toolbox for Microbial and personalized GEM, REactiobiome and community NEtwork modelling☆11Feb 3, 2024Updated 2 years ago
- Supplementary data for co-occurrence manuscript☆10Dec 19, 2019Updated 6 years ago
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆24Jan 24, 2024Updated 2 years ago
- Build a map of genes present across a set of microbial genomes☆18Jan 23, 2026Updated last month
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆18Oct 21, 2022Updated 3 years ago
- Classifiers trained on commonly used variable regions of Prokaryotic 16S rRNA genes☆18Jun 30, 2024Updated last year
- Chimera: A Versatile Metagenomic Classification Tool☆20Feb 1, 2026Updated last month
- R package to predict microbial loads☆17Sep 25, 2025Updated 5 months ago
- ☆44Jun 11, 2025Updated 8 months ago
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆256Jul 27, 2024Updated last year
- Python script to upload bins and MAGs to ENA (European Nucleotide Archive)☆24Feb 12, 2026Updated 2 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆64Apr 10, 2025Updated 10 months ago
- ☆24Dec 5, 2018Updated 7 years ago
- More scalable dereplication for metagenome assembled genomes☆77Dec 17, 2025Updated 2 months ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆30Mar 5, 2019Updated 6 years ago
- Analyses in R and Python Using curatedMetagenomicData☆33Nov 16, 2025Updated 3 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆29Aug 20, 2025Updated 6 months ago
- Metagenomic Estimation of Dietary Intake and Content.☆39Jan 29, 2026Updated last month
- GEne Cluster prediction with COnditional random fields.☆80Jan 24, 2026Updated last month
- Materials and tutorials for the 2020 ISB Microbiome Course☆31Nov 10, 2022Updated 3 years ago
- ☆78Oct 16, 2024Updated last year
- Metagenomics Workshop☆27Nov 23, 2016Updated 9 years ago
- Interactive tools for metagenome visualization and binning in R☆27Jun 28, 2018Updated 7 years ago
- ☆34Sep 5, 2024Updated last year
- From annotated genomes to metabolic screening in large scale microbiotas☆69Jan 16, 2026Updated last month
- ☆32Jan 27, 2026Updated last month
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆11Oct 11, 2022Updated 3 years ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated last year
- MAGScoT - a MAG scoring and refinement tool☆43Oct 10, 2024Updated last year
- Higher-Order Co-occurrence☆12Nov 9, 2021Updated 4 years ago
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- Uncover organisms' metabolic blueprints☆13Jun 18, 2024Updated last year
- Python interface for running COMETS simulations and analyzing the results☆15Updated this week
- Robs manual for the computational genomics and bioinformatics class.☆266Nov 12, 2024Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆47Apr 1, 2025Updated 11 months ago
- Toolbox for comparative genomics of MAGs☆88Updated this week
- Code from the Edwards lab, including bioinformatics, image analysis and more. All this code is created and maintained by folks at Rob Edw…☆42Jan 22, 2026Updated last month
- ☆50Jan 4, 2026Updated last month
- Code and analysis results for the CRC shotgun meta-analysis☆38Sep 28, 2022Updated 3 years ago