knights-lab / SHOGUNLinks
SHallow shOtGUN profiler
☆53Updated 3 years ago
Alternatives and similar repositories for SHOGUN
Users that are interested in SHOGUN are comparing it to the libraries listed below
Sorting:
- Statistical analysis for sparse high-throughput sequencing☆71Updated 11 months ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆47Updated 5 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆57Updated 3 years ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆72Updated 3 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 5 years ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 7 months ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆54Updated 5 months ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆33Updated 5 years ago
- Compare different differential abundance and expression methods☆52Updated 3 years ago
- Computational workflows for metagenomics tasks, by the Bhatt lab☆47Updated 2 years ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆60Updated last year
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆41Updated last year
- Vanilla regression methods for microbiome differential abundance analysis☆60Updated 5 years ago
- Rapid and scalable correlation estimation for compositional data☆95Updated last year
- Sparse Cooccurence Network Investigation for Compositional data☆25Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆61Updated 6 years ago
- ☆79Updated 2 years ago
- ☆23Updated 7 years ago
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆46Updated 3 weeks ago
- A visualization tool for exploratory data analysis of metagenomic data☆37Updated 3 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Updated 3 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆72Updated last year
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Updated 10 months ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 4 months ago
- A toolkit for analyzing and visualizing phylogenetic placement data☆63Updated last month