A pipeline for Bacterial Whole genome sequence data analysis
☆16Jul 24, 2022Updated 3 years ago
Alternatives and similar repositories for BAGEP
Users that are interested in BAGEP are comparing it to the libraries listed below
Sorting:
- ☆10May 14, 2025Updated 9 months ago
- 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
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- Antimicrobial Resistance Analysis☆10Jun 11, 2024Updated last year
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆26Jan 30, 2025Updated last year
- GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples …☆31Feb 27, 2026Updated last week
- Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.☆13Updated this week
- Documentation for analyzing SARS-Cov2 samples.☆12Jun 4, 2020Updated 5 years ago
- A Snakemake pipeline for Quality Control of Whole Genome Sequencing data☆14Jan 18, 2022Updated 4 years ago
- ☆15Nov 28, 2022Updated 3 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- Learning resources originally for a class held December 2020 "Dry bench skills for Researchers". Expanding based upon mini-courses.☆11Jan 27, 2022Updated 4 years ago
- Trim, Align to genome, Deduplicate, Realign WGS sequencing samples☆17Feb 23, 2026Updated last week
- A pipeline for whole genome assembly☆16Apr 21, 2022Updated 3 years ago
- Pipelines for Drosophila genome assembly and analysis☆16May 15, 2022Updated 3 years ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆16Feb 26, 2020Updated 6 years ago
- Various scripts for efficient processing of 10k Salmonella genomes☆16Sep 16, 2021Updated 4 years ago
- Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.☆18May 14, 2018Updated 7 years ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆75Dec 5, 2023Updated 2 years ago
- deduplicate FASTA and FASTQ files☆23Feb 16, 2022Updated 4 years ago
- easy_sbatch - Batch submitting Slurm jobs with script templates☆16Dec 28, 2021Updated 4 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- 把生物信息的一些常用资源整理成一个生信导航网页。☆24Sep 6, 2025Updated 6 months ago
- A utility script to manage local docker instances of HiGlass☆24Jul 6, 2023Updated 2 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data☆20Jan 24, 2022Updated 4 years ago
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated last year
- ☆10Feb 25, 2024Updated 2 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Add new taxa or taxonomic groups to the NCBI Taxdump files☆20Mar 9, 2020Updated 5 years ago
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- whole genome MLST analysis☆51Feb 26, 2026Updated last week
- (current) A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing …☆23Updated this week
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆31Feb 25, 2026Updated last week
- Frequently used commands in Bioinformatics☆23Feb 9, 2026Updated 3 weeks ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub☆25Mar 26, 2022Updated 3 years ago
- Codon Usage Analysis and Prediction of Gene Expressivity☆23Jan 2, 2019Updated 7 years ago