A Hierarchical Approach to Pangenomics Inference
☆13Apr 15, 2024Updated last year
Alternatives and similar repositories for happi
Users that are interested in happi are comparing it to the libraries listed below
Sorting:
- Computation of average nucleotide identity with the use of MMseqs2☆15Dec 11, 2024Updated last year
- Discover and annotate the virome☆59Feb 11, 2026Updated 2 weeks ago
- Hydrocarbon biodegradation gene annotation☆19Jul 14, 2022Updated 3 years ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- ☆13Aug 13, 2024Updated last year
- Snakemake workflow to map and quantify microbial genomes in metagenomic reads☆13Oct 10, 2025Updated 4 months ago
- ☆10Mar 29, 2025Updated 11 months ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year
- Pipeline for identification of eukaryotic contigs in metagenomic assemblies☆13Mar 14, 2024Updated last year
- Integrative virome pipeline☆13Nov 4, 2024Updated last year
- Prediction of microbial interactions in complex communities☆11Aug 14, 2024Updated last year
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Jan 23, 2026Updated last month
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆27Jul 22, 2024Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆54Sep 7, 2025Updated 5 months ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆14Jul 14, 2024Updated last year
- A wrapper to identify, bin, classify, and predict host-viral relationship for viruses☆87Dec 27, 2024Updated last year
- ☆57Feb 18, 2026Updated last week
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆60Nov 3, 2023Updated 2 years ago
- Various scripts used at the EnvGen group, directed towards metagenomic analysis.☆15Apr 28, 2020Updated 5 years ago
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆71Feb 5, 2026Updated 3 weeks ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆17Nov 24, 2025Updated 3 months ago
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Dec 9, 2025Updated 2 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 8 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Apr 1, 2023Updated 2 years ago
- R tools for reconstructing metabolisms.☆14Feb 13, 2026Updated 2 weeks ago
- Protocol for finding informative protein families and then using them to score omic samples☆18Jul 27, 2022Updated 3 years ago
- pyRforest: A comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R☆14Aug 20, 2024Updated last year
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆49Updated this week
- Prefix-renaming FASTA records really fast.☆17Jun 26, 2024Updated last year
- Variant call verification☆16May 12, 2025Updated 9 months ago
- ☆21Mar 15, 2023Updated 2 years ago
- Binning Virus Genomes from Metagenomes☆72Jul 13, 2022Updated 3 years ago
- ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.☆18Aug 16, 2021Updated 4 years ago
- Assign taxonomy with blast, can be used for qiime☆25Mar 25, 2025Updated 11 months ago
- VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data☆23Oct 21, 2025Updated 4 months ago
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 3 months ago
- ☆49Mar 13, 2024Updated last year
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆82Sep 8, 2025Updated 5 months ago