A pipeline for Bacterial Whole genome sequence data analysis
☆15Jul 24, 2022Updated 4 years ago
Alternatives and similar repositories for BAGEP
Users that are interested in BAGEP are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆11May 14, 2025Updated last year
- Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical bi…☆18Sep 1, 2023Updated 2 years ago
- Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)☆12Aug 6, 2023Updated 2 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data☆20Jan 24, 2022Updated 4 years ago
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆27Jan 30, 2025Updated last year
- Antimicrobial Resistance Analysis☆10Jun 11, 2024Updated 2 years ago
- A pipeline for whole genome assembly☆16Apr 21, 2022Updated 4 years ago
- Documentation for analyzing SARS-Cov2 samples.☆12Jun 4, 2020Updated 6 years ago
- GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples …☆32May 18, 2026Updated 2 months ago
- Add new taxa or taxonomic groups to the NCBI Taxdump files☆20Mar 9, 2020Updated 6 years ago
- Various scripts for efficient processing of 10k Salmonella genomes☆16Sep 16, 2021Updated 4 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆79Dec 5, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆29Jul 21, 2025Updated last year
- 把生物信息的一些常用资源整理成一个生信导航网页。☆23Sep 6, 2025Updated 10 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- whole genome MLST analysis☆55Jun 17, 2026Updated last month
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- Mycobacterial pipeline☆11Sep 11, 2025Updated 10 months ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 5 years ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- A Snakemake pipeline for Quality Control of Whole Genome Sequencing data☆14Jan 18, 2022Updated 4 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.☆18May 14, 2018Updated 8 years ago
- A utility script to manage local docker instances of HiGlass☆24Jul 6, 2023Updated 3 years ago
- Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.☆15Jul 6, 2026Updated 2 weeks ago
- AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below s…☆11Jun 24, 2026Updated last month
- ☆15Nov 28, 2022Updated 3 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆21Oct 8, 2025Updated 9 months ago
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- Public repository for the biodata resource inventory performed in 2022.☆11Nov 25, 2025Updated 8 months ago
- (current) A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing …☆22Jul 8, 2026Updated 2 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆35Jul 2, 2024Updated 2 years ago
- Rapid discovery of novel prophages using biological feature engineering and machine learning☆39Dec 20, 2024Updated last year
- Codon Usage Analysis and Prediction of Gene Expressivity☆23Jan 2, 2019Updated 7 years ago
- Pipelines for Drosophila genome assembly and analysis☆16May 15, 2022Updated 4 years ago
- Trim, Align to genome, Deduplicate, Realign WGS sequencing samples☆17Feb 23, 2026Updated 5 months ago
- Hierarchical clustering of cgMLST☆13Nov 20, 2023Updated 2 years ago
- circlize examples☆11Jun 23, 2020Updated 6 years ago