Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
☆62Apr 1, 2023Updated 2 years ago
Alternatives and similar repositories for MAGpy
Users that are interested in MAGpy are comparing it to the libraries listed below
Sorting:
- A Hierarchical Approach to Pangenomics Inference☆13Apr 15, 2024Updated last year
- DAS Tool☆167May 2, 2024Updated last year
- Toolbox for comparative genomics of MAGs☆88Feb 24, 2026Updated 3 weeks ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆78Jun 17, 2024Updated last year
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 8 months ago
- Annotate your metagenome assemblies☆11Jul 19, 2018Updated 7 years ago
- Open prediction of Polysaccharide Utilisation Loci (PUL)☆25Apr 22, 2020Updated 5 years ago
- Bioinformatics program inStrain☆182Mar 12, 2026Updated last week
- A toolbox for improving metagenome-assembled genomes.☆64Jun 2, 2021Updated 4 years ago
- CAMITAX: Taxon labels for microbial genomes☆31Dec 14, 2023Updated 2 years ago
- Long-read metagenomic analysis☆110Oct 10, 2023Updated 2 years ago
- Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database☆10Dec 16, 2016Updated 9 years ago
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆72Mar 3, 2026Updated 2 weeks ago
- Analysis pipeline for functional metagenomic sequencing data obtained using nanopore sequencing☆12Nov 20, 2016Updated 9 years ago
- A Perl pipeline for identifying marker genes and build phylogenetic trees for a set of genomes☆14Jun 19, 2017Updated 8 years ago
- A set of scripts to help automate the construction of data sets for multi-gene phylogenetic analyses.☆13Mar 13, 2019Updated 7 years ago
- ATLAS - Three commands to start analyzing your metagenome data☆403Nov 28, 2025Updated 3 months ago
- reference-based long read assemblies of bacterial genomes☆51Aug 9, 2021Updated 4 years ago
- Deep learning library for biological sequences. Extension of Fastai and Pytorch.☆39May 30, 2025Updated 9 months ago
- Set of utilities on sequences and BAM files☆27Oct 27, 2021Updated 4 years ago
- Microbiome classification pipeline☆67May 13, 2025Updated 10 months ago
- Variational autoencoder for metagenomic binning☆319Feb 23, 2026Updated 3 weeks ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆240Oct 12, 2025Updated 5 months ago
- Protocol for finding informative protein families and then using them to score omic samples☆18Jul 27, 2022Updated 3 years ago
- De novo assembly of nanopore reads using nextflow☆20Aug 5, 2020Updated 5 years ago
- SemiBin: metagenomics binning with self-supervised deep learning☆156Feb 19, 2026Updated last month
- a pipeline to cluster proteins into families☆10Apr 1, 2020Updated 5 years ago
- Read alignment statistics for metagenomics☆390Jan 16, 2026Updated 2 months ago
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads☆68Nov 4, 2021Updated 4 years ago
- GraftM - Rapid community profiles from metagenomes☆50Nov 6, 2025Updated 4 months ago
- A complete pipeline for metagenomic analysis☆440Mar 11, 2026Updated last week
- GTDB taxonomy taxdump files with trackable TaxIds☆57Apr 29, 2025Updated 10 months ago
- Hydrocarbon biodegradation gene annotation☆19Jul 14, 2022Updated 3 years ago
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆124Aug 24, 2023Updated 2 years ago
- Indexing & querying large assembly graphs -- in space, no one can hear you miao!☆118Jan 29, 2026Updated last month
- Tool (experimental) to compute layout from overlaps with spectral algorithm☆11Nov 28, 2017Updated 8 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Updated this week
- Assessing the quality of metagenome-derived genome bins using machine learning☆252Mar 20, 2025Updated last year