ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
☆31Jan 24, 2025Updated last year
Alternatives and similar repositories for shortbred
Users that are interested in shortbred are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Software used to develop the TCMA database associated with 10.1016/j.chom.2020.12.001.☆15Nov 26, 2023Updated 2 years ago
- ☆12Jan 29, 2020Updated 6 years ago
- ☆29Aug 2, 2026Updated last week
- Batch effects removal for microbiome data via conditional quantile regression☆33Aug 23, 2022Updated 3 years ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆94May 11, 2026Updated 3 months 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.
- MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.☆16Mar 2, 2023Updated 3 years ago
- A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deep…☆58Apr 30, 2026Updated 3 months ago
- http://huttenhower.sph.harvard.edu/waafle☆24Jun 16, 2026Updated last month
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆45Apr 8, 2024Updated 2 years ago
- ☆20Nov 11, 2024Updated last year
- Identify and remove contaminants from metagenome-assembled genomes☆18Feb 16, 2024Updated 2 years ago
- ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Dat…☆75Mar 16, 2025Updated last year
- A toolbox for comparative genomics.☆110May 26, 2021Updated 5 years ago
- AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…☆57Jul 26, 2026Updated 2 weeks 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.
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆26Jun 9, 2021Updated 5 years ago
- A method for reconstruction of subspecies composition and functional profiles from metagenomic data☆13May 27, 2024Updated 2 years ago
- EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for cli…☆28Updated this week
- Short Read Sequence Typing for Bacterial Pathogens☆150Jun 20, 2021Updated 5 years ago
- ☆37Nov 11, 2022Updated 3 years ago
- Find Co-Abundant Groups of Genes☆12Aug 3, 2020Updated 6 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆38Feb 26, 2023Updated 3 years ago
- ☆38Nov 5, 2025Updated 9 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆60Nov 3, 2023Updated 2 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.
- ☆17Dec 5, 2017Updated 8 years ago
- 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
- SemiBin: metagenomics binning with self-supervised deep learning☆174Aug 3, 2026Updated last week
- A microbial profiling framework for metagenomic analysis☆24Apr 9, 2020Updated 6 years ago
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆250Jul 10, 2026Updated last month
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing☆20May 11, 2022Updated 4 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆66Jun 7, 2023Updated 3 years ago
- MGnify genome analysis pipeline☆115Updated this week
- More scalable dereplication for metagenome assembled genomes☆87Aug 3, 2026Updated last week
- 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.
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated last year
- Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and …☆10Jun 19, 2019Updated 7 years ago
- code repo for mobileOG-db☆49Jul 30, 2026Updated 2 weeks ago
- ☆22Mar 25, 2014Updated 12 years ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆174Sep 4, 2025Updated 11 months ago
- ☆28May 22, 2025Updated last year
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆428May 20, 2026Updated 2 months ago