Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
☆36May 1, 2023Updated 2 years ago
Alternatives and similar repositories for Shotgun-Metagenomics-Analysis
Users that are interested in Shotgun-Metagenomics-Analysis are comparing it to the libraries listed below
Sorting:
- Unified Human Gut Virome Catalog☆41Nov 10, 2025Updated 4 months ago
- Personal notes about work- and coding-related topics☆21Mar 22, 2023Updated 2 years ago
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated 7 months ago
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13May 12, 2022Updated 3 years ago
- A taxonomic classifier for shotgun metagenomics reads☆11Apr 4, 2025Updated 11 months ago
- A repo to reproduce the experiments in the YACHT manuscript☆11Nov 2, 2023Updated 2 years ago
- Automated pipeline for whole bacterial genome analysis based on snakemake☆12May 16, 2022Updated 3 years ago
- Metagenomics Workshop☆27Nov 23, 2016Updated 9 years ago
- GitHub template repository for creating new barebones Nextflow pipelines, using the Arcadia-Science/nextflow-template cookiecutter templa…☆13Mar 21, 2023Updated 2 years ago
- ☆20Jun 12, 2023Updated 2 years ago
- Bioinformatics Guide☆17Jul 25, 2021Updated 4 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆40Feb 9, 2022Updated 4 years ago
- Identify and remove contaminants from metagenome-assembled genomes☆18Feb 16, 2024Updated 2 years ago
- Metagenomic pipeline managed by snakemake☆18Sep 18, 2024Updated last year
- A DRAFT, early stage book on snakemake.☆22Nov 1, 2023Updated 2 years ago
- A snakemake workflow for metagenomic projects☆15Feb 16, 2023Updated 3 years ago
- ☆17Mar 11, 2018Updated 7 years ago
- This is a read-only mirror of the CRAN R package repository. TOmicsVis — Transcriptome Visualization Process Scheme. Homepage: https://…☆16Aug 28, 2023Updated 2 years ago
- A functional profiler for metagenomes using FracMinHash☆21Jul 14, 2025Updated 7 months ago
- HoCoRT - Remove specific organisms from sequencing reads☆17Jan 5, 2025Updated last year
- Workshop materials for the Second Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop at the TAMUCC Harte Institute in Corpu…☆22Jan 19, 2018Updated 8 years ago
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Feb 12, 2026Updated 3 weeks ago
- A microbiome analysis toolkit for R☆25Aug 21, 2023Updated 2 years ago
- RNAseq analysis in R workshop, originally taught: http://combine-australia.github.io/2016-05-11-RNAseq/☆24Dec 1, 2020Updated 5 years ago
- Creating plasmid maps inside ggplot.☆91Sep 2, 2025Updated 6 months ago
- ☆23Apr 20, 2023Updated 2 years ago
- Accurate identification of bacteriophages from metagenomic data using Transformer☆22Nov 6, 2024Updated last year
- Repo for student website☆28Feb 22, 2026Updated 2 weeks ago
- Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.☆26Feb 14, 2026Updated 3 weeks ago
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆37Feb 17, 2026Updated 3 weeks ago
- Detect contigs of complete circular genomes☆23Jun 6, 2019Updated 6 years ago
- Gene expression meta-analysis visualization tool☆22Aug 10, 2023Updated 2 years ago
- GenoVi, an automated customizable circular genome visualizer for bacteria and archaea☆103Jun 25, 2023Updated 2 years ago
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated 2 weeks ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 3 years ago
- Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data☆23Jun 27, 2022Updated 3 years ago
- R implementation of the LEfSe method☆63Nov 17, 2025Updated 3 months ago
- Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries☆12Jan 4, 2026Updated 2 months ago