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☆69Updated 9 months 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
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 3 months ago
- ☆23Updated 7 years ago
- Sparse Cooccurence Network Investigation for Compositional data☆25Updated 11 months ago
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 5 months 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…☆55Updated 3 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 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
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆45Updated 5 years ago
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆46Updated 3 weeks ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago
- An ultrafast optimal aligner for mapping large NGS data to large genome databases.☆57Updated last year
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆58Updated last year
- ☆78Updated last year
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 2 months ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆64Updated last year
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆39Updated last year
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- BEAV: Bacterial Element Annotation reVamped☆69Updated last month
- MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.☆16Updated 2 years ago
- Massively parallel phylogenetic placement of genetic sequences☆84Updated 3 years ago
- Rapid and scalable correlation estimation for compositional data☆93Updated last year
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆49Updated last year
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- StrainFinder☆27Updated 7 years ago