Metagenome read simulation of multiple synthetic communities
☆10Jan 6, 2024Updated 2 years ago
Alternatives and similar repositories for MGSIM
Users that are interested in MGSIM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A functional profiler for metagenomes using FracMinHash☆22Apr 20, 2026Updated 6 months ago
- Gupta et al., TaxiBGC: a Taxonomy-guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Sec…☆16May 24, 2023Updated 3 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆29Feb 6, 2023Updated 3 years ago
- MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome☆18Nov 7, 2019Updated 6 years ago
- A repo to reproduce the experiments in the YACHT manuscript☆12Nov 2, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆14Jan 8, 2020Updated 6 years ago
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆43Updated this week
- Repository for codes, analyses and visualizations for the CAMI II challenges☆15Sep 4, 2023Updated 3 years ago
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆25Mar 19, 2023Updated 3 years ago
- ☆16Jun 2, 2021Updated 5 years ago
- Code used to analyse and plot metadata of metagenomic binning tools☆14Aug 22, 2024Updated 2 years ago
- Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination☆15Aug 20, 2026Updated 2 months ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆16Jun 26, 2018Updated 8 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- NGSNGS: Next generation simulator for next generation sequencing data☆58Nov 27, 2024Updated last year
- The Microbial Co-occurrence Network Explorer☆21Oct 17, 2023Updated 3 years ago
- Pan-genome Analysis☆14May 4, 2025Updated last year
- ☆19Nov 15, 2025Updated 11 months ago
- Chimera: A Versatile Metagenomic Classification Tool☆21Oct 20, 2026Updated last week
- mSWEEP High-resolution sweep metagenomics using fast probabilistic inference☆18Nov 19, 2025Updated 11 months ago
- EnDED is a program that aims to detect environmentally-driven ("indirect") edges in an association network.☆10Dec 1, 2023Updated 2 years ago
- ☆20Nov 11, 2024Updated last year
- ARBitR: Assembly Refinement with Barcode-identity-tagged Reads☆10Oct 22, 2020Updated 6 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Chang and Gupta et al., Gut Microbiome Wellness Index 2 Enhances Health Status Prediction from Gut Microbiome Taxonomic Profiles, Nature …☆27Jan 20, 2025Updated last year
- SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.☆28Nov 19, 2025Updated 11 months ago
- A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA☆14Apr 16, 2025Updated last year
- Computation of Unifrac using Earth Movers Distance☆10Jun 20, 2022Updated 4 years ago
- A tool for representing genomic potential and transcriptomic expression into KEGG pathways☆63Jul 28, 2024Updated 2 years ago
- kmer-based software for detecting bacterial strain genomes inside metagenomes☆12Dec 11, 2024Updated last year
- Hybrid Error Correction of Long Reads using Iterative Learning☆10Sep 27, 2018Updated 8 years ago
- BiG-MEx implementation as Docker images and R packages☆13Feb 9, 2022Updated 4 years ago
- Animations of tidyverse verbs using R, the tidyverse, and gganimate☆13Sep 22, 2019Updated 7 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆34Nov 28, 2023Updated 2 years ago
- Run shell commands in a scientifically reproducible and robust way☆35Sep 11, 2026Updated last month
- Parser and annotation tools using the FAPROTAX database (Louca S. et al., 2016)☆13Apr 8, 2022Updated 4 years ago
- Compute strain abundance in a defined microbial community☆10Jul 27, 2023Updated 3 years ago
- A pathway profiling tool designed for traversing metabolic pathway graphs, identifying most complete paths based on an evaluation set of …☆11Sep 10, 2026Updated last month
- Phase 2 repo for the Inserm Workshop on Machine Learning in Biology☆19Dec 17, 2025Updated 10 months ago
- ☆47Jun 27, 2023Updated 3 years ago