scripts for estimating bacteria replication rates based on population genome copy number variation
☆75Dec 28, 2019Updated 6 years ago
Alternatives and similar repositories for iRep
Users that are interested in iRep are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32May 22, 2020Updated 6 years ago
- Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset☆20May 22, 2020Updated 6 years ago
- Improvement of metagenome-assembled genomes☆57Mar 17, 2020Updated 6 years ago
- A toolbox for improving metagenome-assembled genomes.☆64Jun 2, 2021Updated 5 years ago
- Estimate metagenomic coverage and sequence diversity☆62Jun 26, 2026Updated 3 weeks ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ☆56Mar 29, 2026Updated 3 months ago
- StrainFinder☆30Jul 8, 2018Updated 8 years ago
- A scalable high-throughput metabolic and biogeochemical functional trait profiler☆227Mar 24, 2026Updated 3 months ago
- Variational autoencoder for metagenomic binning☆330Apr 27, 2026Updated 2 months ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆46Feb 17, 2023Updated 3 years ago
- A tool to assemble high-quality phages from metagenomes.☆17May 22, 2026Updated last month
- A hybrid assembly and MAG recovery pipeline (and more!)☆109Jul 10, 2026Updated last week
- Python script to upload bins and MAGs to ENA (European Nucleotide Archive)☆24Updated this week
- Virus Identification By iteRative ANnoTation☆198Apr 15, 2024Updated 2 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- DAS Tool☆177May 2, 2024Updated 2 years ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆271Mar 20, 2025Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆68Aug 12, 2019Updated 6 years ago
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing☆20May 11, 2022Updated 4 years ago
- Software for prediction of plasmid sequences in metagenomic assemblies☆111Jun 28, 2021Updated 5 years ago
- A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data☆101Aug 11, 2025Updated 11 months ago
- ☆18Mar 11, 2024Updated 2 years ago
- SemiBin: metagenomics binning with self-supervised deep learning☆172Updated this week
- Automatic eukaryotic taxonomic classification☆33May 9, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆22Jul 8, 2024Updated 2 years ago
- ☆47Jun 27, 2023Updated 3 years ago
- This is a repository for CAMPER.☆17Mar 18, 2024Updated 2 years ago
- KEGG Module Evaluation Tool☆33Mar 5, 2026Updated 4 months ago
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆77Jul 13, 2026Updated last week
- antiSMASH☆259Jun 29, 2026Updated 3 weeks ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆314Feb 3, 2026Updated 5 months ago
- Identifying viruses from metagenomic data by deep learning☆154May 5, 2026Updated 2 months ago
- StrainEst - abundance estimation of strains☆20Jan 17, 2020Updated 6 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆615May 20, 2026Updated 2 months ago
- Bioinformatics program inStrain☆191Mar 12, 2026Updated 4 months ago
- Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes☆192Updated this week
- De novo Extraction of Strains from MetAgeNomes☆72Jun 17, 2020Updated 6 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆24May 14, 2023Updated 3 years ago
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆124May 29, 2026Updated last month
- EMIRGE reconstructs full length ribosomal genes from short read sequencing data.☆38Sep 15, 2023Updated 2 years ago