Accurate and robust inference of microbial growth dynamics from metagenomic sequencing
☆19May 11, 2022Updated 3 years ago
Alternatives and similar repositories for coptr
Users that are interested in coptr are comparing it to the libraries listed below
Sorting:
- Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset☆19May 22, 2020Updated 5 years ago
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins☆15Dec 7, 2021Updated 4 years ago
- snapper☆13Jul 8, 2024Updated last year
- Plot microbiome time series in parallel☆27Nov 7, 2023Updated 2 years ago
- Scatterbar - data visualization for proportional data across many spatially resolved coordinates☆11Mar 3, 2025Updated last year
- ☆26Jan 30, 2025Updated last year
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32May 22, 2020Updated 5 years ago
- Database and pipeline for protein structure-guided annotations of ecologically relevant functions at the metagenome scale.☆24Nov 2, 2025Updated 4 months ago
- ☆12Jul 21, 2025Updated 8 months ago
- Python script to upload bins and MAGs to ENA (European Nucleotide Archive)☆24Feb 12, 2026Updated last month
- ☆81Mar 13, 2026Updated last week
- Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome☆68Mar 28, 2025Updated 11 months ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆74Updated this week
- ☆25Jun 20, 2023Updated 2 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆74Dec 28, 2019Updated 6 years ago
- Minimal Microbial Consortia creation tools☆13Jan 28, 2022Updated 4 years ago
- PaperBLAST: find papers about a protein or its homologs☆51Mar 11, 2026Updated last week
- Discovery of conserved gene clusters in multiple genomes☆125Jan 16, 2026Updated 2 months ago
- Phasing for metagenomics using PacBio long reads☆16Jul 14, 2021Updated 4 years ago
- a simple tool for listing conda environments with descriptions☆14Mar 28, 2025Updated 11 months ago
- MAG Circularization Method☆32Nov 4, 2025Updated 4 months ago
- Metagenomic Binning Algorithm☆51Jan 16, 2026Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆54Sep 7, 2025Updated 6 months ago
- ☆32Jan 4, 2025Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆47Feb 5, 2026Updated last month
- Automatic eukaryotic taxonomic classification☆29May 9, 2025Updated 10 months ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆104Jan 27, 2026Updated last month
- ☆53May 5, 2025Updated 10 months ago
- ☆50Jan 4, 2026Updated 2 months ago
- ☆20Apr 24, 2025Updated 10 months ago
- ☆22Dec 9, 2023Updated 2 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆48Apr 14, 2020Updated 5 years ago
- ☆14Oct 14, 2023Updated 2 years ago
- ☆44Jun 11, 2025Updated 9 months ago
- ☆38Dec 6, 2023Updated 2 years ago
- Quality assessment of de novo transcriptome assemblies from RNA-Seq data☆26Nov 14, 2025Updated 4 months ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆17Nov 24, 2025Updated 3 months ago
- SMBGC Annotation using Neural Networks Trained on Interpro Signatures☆30Mar 9, 2026Updated last week
- 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes☆81Dec 4, 2025Updated 3 months ago