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 last year
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆55Updated 7 months ago
- Computational workflows for metagenomics tasks, by the Bhatt lab☆47Updated 2 years ago
- Compare different differential abundance and expression methods☆52Updated 3 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆34Updated 5 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
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- Sparse Cooccurence Network Investigation for Compositional data☆25Updated last year
- A set of R scripts for the analysis of microbial profiles☆41Updated last week
- 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
- Automated pipeline for analyses of fungal ITS from the Illumina☆32Updated 8 months ago
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆42Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆64Updated 6 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆61Updated last year
- Metagenomics Workshop☆28Updated 9 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆47Updated 5 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 6 years ago
- ☆18Updated 3 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆51Updated 3 years ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- ☆61Updated last month
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆46Updated 3 weeks ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Updated 11 months ago
- ☆78Updated 2 years ago
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆50Updated last year
- ☆23Updated 7 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆66Updated 2 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆78Updated 5 months ago