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.☆14Nov 26, 2023Updated 2 years ago
- ☆12Jan 29, 2020Updated 6 years ago
- ☆26Jan 30, 2025Updated last year
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆82Mar 12, 2026Updated 2 weeks ago
- Batch effects removal for microbiome data via conditional quantile regression☆32Aug 23, 2022Updated 3 years ago
- 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.
- MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.☆16Mar 2, 2023Updated 3 years ago
- http://huttenhower.sph.harvard.edu/waafle☆23Feb 26, 2026Updated last month
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆43Apr 8, 2024Updated last year
- ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Dat…☆72Mar 16, 2025Updated last year
- ☆19Nov 11, 2024Updated last year
- Identify and remove contaminants from metagenome-assembled genomes☆18Feb 16, 2024Updated 2 years ago
- A toolbox for comparative genomics.☆109May 26, 2021Updated 4 years ago
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆24Jun 9, 2021Updated 4 years ago
- 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
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Find Co-Abundant Groups of Genes☆11Aug 3, 2020Updated 5 years ago
- ☆36Nov 11, 2022Updated 3 years ago
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆403Mar 18, 2026Updated last week
- Short Read Sequence Typing for Bacterial Pathogens☆145Jun 20, 2021Updated 4 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆37Feb 26, 2023Updated 3 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆60Nov 3, 2023Updated 2 years ago
- ☆36Nov 5, 2025Updated 4 months ago
- 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
- A method for reconstruction of subspecies composition and functional profiles from metagenomic data☆13May 27, 2024Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- A microbial profiling framework for metagenomic analysis☆24Apr 9, 2020Updated 5 years ago
- ☆17Dec 5, 2017Updated 8 years ago
- SemiBin: metagenomics binning with self-supervised deep learning☆156Feb 19, 2026Updated last month
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆237Jan 20, 2026Updated 2 months ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 9 months ago
- MGnify genome analysis pipeline☆109Updated this week
- OPERA-MS - Hybrid Metagenomic Assembler☆99Jul 3, 2024Updated 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 6 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆67Jun 7, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- ☆22Mar 25, 2014Updated 12 years ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆170Sep 4, 2025Updated 6 months ago
- Bioinformatics program inStrain☆182Mar 12, 2026Updated 2 weeks ago
- Profiler for metagenomics based on NGLess☆13Feb 22, 2024Updated 2 years ago
- Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes☆183Mar 19, 2026Updated last week
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆54Sep 7, 2025Updated 6 months ago
- IPHOMED☆11Jun 11, 2025Updated 9 months ago