Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
☆32May 22, 2020Updated 5 years ago
Alternatives and similar repositories for GRiD
Users that are interested in GRiD are comparing it to the libraries listed below
Sorting:
- scripts for estimating bacteria replication rates based on population genome copy number variation☆74Dec 28, 2019Updated 6 years ago
- Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset☆19May 22, 2020Updated 5 years ago
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆21Jul 8, 2024Updated last year
- ☆50Jan 4, 2026Updated 2 months ago
- Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species☆18Mar 17, 2021Updated 5 years ago
- MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-thro…☆26Nov 14, 2022Updated 3 years ago
- Scripts for calculating features and regression of prokaryote OGT☆25Feb 13, 2024Updated 2 years ago
- This is a comprehensive database for fast and accurately analyzing the phosphorus cycling genes.☆34Jul 12, 2022Updated 3 years ago
- ☆22Apr 3, 2023Updated 2 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆14Aug 26, 2024Updated last year
- A scalable high-throughput metabolic and biogeochemical functional trait profiler☆219Jan 27, 2025Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆65Aug 12, 2019Updated 6 years ago
- Phasing for metagenomics using PacBio long reads☆16Jul 14, 2021Updated 4 years ago
- Python package to study microbial communities using metabolic modeling.☆121Mar 11, 2026Updated last week
- Toolbox for comparative genomics of MAGs☆88Feb 24, 2026Updated 3 weeks ago
- Horizontal gene transfer (HGT) identification pipeline☆69May 17, 2023Updated 2 years ago
- statdivlab's teaching materials for STAMPS @ the MBL in 2019☆11Jul 28, 2019Updated 6 years ago
- Genome-informed, trait-based dynamic energy budget modeling of microbes with ML analysis of emergent strategies☆18Feb 18, 2026Updated last month
- Mapping-Assisted Targeted-Assembly for Metagenomics☆26Mar 28, 2025Updated 11 months ago
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing☆19May 11, 2022Updated 3 years ago
- Fast alignment-free pangenome creation and exploration☆28Apr 16, 2020Updated 5 years ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆43Feb 17, 2023Updated 3 years ago
- Parser for Ghost Koala☆10Aug 23, 2018Updated 7 years ago
- A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.☆28Feb 14, 2023Updated 3 years ago
- ☆26Jan 30, 2025Updated last year
- A healthy human gut genome collection☆25Aug 21, 2025Updated 7 months ago
- Python script to upload bins and MAGs to ENA (European Nucleotide Archive)☆24Feb 12, 2026Updated last month
- KEGG Module Evaluation Tool☆33Mar 5, 2026Updated 2 weeks ago
- ☆49Mar 13, 2024Updated 2 years ago
- A QIIME 2 plugin for interaction with the Greengenes2 database☆33Oct 1, 2024Updated last year
- A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deep…☆55Nov 15, 2023Updated 2 years ago
- SMETANA: a tool to analyse interactions in microbial communities☆67May 6, 2025Updated 10 months ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs☆17Feb 5, 2022Updated 4 years ago
- The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of …☆21Oct 2, 2025Updated 5 months ago
- Integrated Network Analysis Pipeline☆18Dec 19, 2024Updated last year
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated 2 years ago
- Similarity networks of biosynthetic gene clusters☆157Updated this week
- some useful scripts for working with genomics and sequencing data☆17Oct 31, 2019Updated 6 years ago