olabiyi / snakemake-workflow-qiime2Links
Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2
☆16Updated last year
Alternatives and similar repositories for snakemake-workflow-qiime2
Users that are interested in snakemake-workflow-qiime2 are comparing it to the libraries listed below
Sorting:
- Batch effects removal for microbiome data via conditional quantile regression☆31Updated 3 years ago
- A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.☆28Updated 6 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆54Updated 2 months ago
- Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project☆12Updated 3 years ago
- R package to predict microbial loads☆16Updated 2 months ago
- Pipeline & Reproducible analysis examples for amplicon and metagenome in microbiome☆41Updated 5 years ago
- Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.…☆34Updated 4 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆66Updated 2 years ago
- Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.☆32Updated 2 years ago
- ☆32Updated 2 years ago
- Make a non-redundant, comprehensive COI database from NCBI and BOLD and include customizing options☆16Updated 3 months ago
- ☆57Updated last year
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆30Updated 5 years ago
- This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interacti…☆33Updated 3 years ago
- ☆15Updated 2 years ago
- gutSMASH☆55Updated 8 months ago
- This is the supplementary code for CRC-multi-kingdom☆17Updated 3 years ago
- Code and analysis results for the CRC shotgun meta-analysis☆39Updated 2 years ago
- repo for cicese metatranscriptomics workshop, nov 2018☆14Updated 5 years ago
- ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…☆32Updated 7 months ago
- ☆13Updated 8 months ago
- Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groning…☆58Updated 3 months ago
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆121Updated last year
- ☆24Updated 5 years ago
- Analysing Metagenomic Species (MGS)☆41Updated 4 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆56Updated 3 years ago
- Statistical analysis for sparse high-throughput sequencing☆69Updated 8 months ago
- A shiny package for microbiome functional enrichment analysis☆36Updated 4 months ago
- Metagenomics Taxonomic Reads Assembly Single-Species☆16Updated 2 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago