A nextflow pipeline for performing bacterial RNA-Seq data analysis.
☆12Oct 14, 2025Updated 5 months ago
Alternatives and similar repositories for BactSeq
Users that are interested in BactSeq are comparing it to the libraries listed below
Sorting:
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆22Apr 16, 2024Updated last year
- A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments☆11Dec 1, 2020Updated 5 years ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Feb 6, 2018Updated 8 years ago
- Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram☆12Mar 10, 2026Updated last week
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated 2 years ago
- mSWEEP High-resolution sweep metagenomics using fast probabilistic inference☆15Nov 19, 2025Updated 4 months ago
- ☆13Sep 4, 2017Updated 8 years ago
- ☆13Updated this week
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated last year
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Feb 12, 2016Updated 10 years ago
- transposable element typing pipeline☆19Mar 8, 2024Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- Omics data analysis☆16Feb 25, 2026Updated 3 weeks ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated 2 years ago
- Bioinformatics tool to find integrons in bacterial genomes☆86May 7, 2025Updated 10 months ago
- ☆22Apr 3, 2023Updated 2 years ago
- Code repository for machine learning and computational analysis of large-scale microbial genomics data (https://rdcu.be/9rHj)☆20May 12, 2025Updated 10 months ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Apr 20, 2023Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆24Aug 1, 2025Updated 7 months ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 1, 2026Updated 3 weeks ago
- Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣☆11Apr 28, 2023Updated 2 years ago
- Code for detecting genomic island insertions in clades of microbes.☆19Sep 14, 2023Updated 2 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Apr 11, 2018Updated 7 years ago
- A command line tool to compute mapping statistics from a BAM file☆25Mar 7, 2022Updated 4 years ago
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated last month
- A toolkit for prokaryotic comparative genomics☆51Feb 23, 2026Updated 3 weeks ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- ☆22Jul 28, 2025Updated 7 months ago
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- Get microbial sequence data easier and faster☆28Nov 7, 2019Updated 6 years ago
- GC Skew Test for Bacterial Genomes☆32Sep 29, 2022Updated 3 years ago
- ☆14Mar 8, 2021Updated 5 years ago
- R CRAN package `diptest` : Hartigan's diptest for unimodality (including p-values)☆11Aug 19, 2025Updated 7 months ago
- This tool estimates the completeness of KEGG pathway modules from the presence or absence of KEGG orthologues (KOs)☆33Jan 19, 2026Updated 2 months ago
- ☆10Dec 12, 2017Updated 8 years ago
- IAN: An Intelligent System for Omics Data Analysis and Discovery☆10Feb 23, 2026Updated 3 weeks ago
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 6 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago