biobakery / shortbred
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.
☆28Updated 3 weeks ago
Alternatives and similar repositories for shortbred:
Users that are interested in shortbred are comparing it to the libraries listed below
- Set of utilities on sequences and BAM files☆26Updated 3 years ago
- ☆22Updated 5 years ago
- OPAL: Open-community Profiling Assessment tooL☆28Updated last month
- Improvement of metagenome-assembled genomes☆51Updated 4 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆20Updated 3 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆26Updated 2 weeks ago
- MAG Circularization Method☆33Updated 2 years ago
- A metagenomic strategy for harnessing the chemical repertoire of the human microbiome☆32Updated last year
- Gene-flank analysis tool☆27Updated 2 months ago
- A repository for the lessons and notebooks used for Binder tutorials☆13Updated 4 years ago
- HoCoRT - Remove specific organisms from sequencing reads☆16Updated last month
- ☆32Updated last year
- KEGG Module Evaluation Tool☆28Updated last year
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- Workflows for metagenomic sequence data processing and analysis.☆17Updated 5 years ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated 3 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated 3 weeks ago
- MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.☆14Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 2 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated last year
- ☆19Updated 4 years ago
- ☆20Updated 8 years ago
- ☆16Updated 4 years ago
- MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome☆21Updated 4 months ago
- IslandPath standalone software☆31Updated last year
- ☆28Updated last month