biobakery / shortbredLinks
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.
☆31Updated 9 months ago
Alternatives and similar repositories for shortbred
Users that are interested in shortbred are comparing it to the libraries listed below
Sorting:
- Analysing Metagenomic Species (MGS)☆42Updated 4 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆64Updated last month
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆35Updated last month
- A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations☆43Updated 2 years ago
- ☆40Updated 4 years ago
- ☆32Updated 9 months ago
- Discover and annotate the virome☆53Updated 2 weeks ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆42Updated 5 years ago
- MAG Circularization Method☆32Updated 3 years ago
- Improvement of metagenome-assembled genomes☆54Updated 5 years ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆39Updated 2 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated 2 weeks ago
- Set of utilities on sequences and BAM files☆26Updated 4 years ago
- http://huttenhower.sph.harvard.edu/waafle☆22Updated 10 months ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆37Updated last year
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆39Updated last year
- ☆42Updated last year
- Pangenome analysis of eukaryotes.☆19Updated 5 years ago
- Scalable creating/updating of metagenome profiling databases☆62Updated 4 months ago
- Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes☆22Updated 2 years ago
- ☆79Updated last week
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 3 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 3 months ago
- ☆30Updated 2 weeks ago
- Accurate metagenomi/metatranscriptomic analysis pipeline☆23Updated 4 years ago
- hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.☆69Updated this week
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago