jizhang-nz / fast-GePView external linksLinks
Fast genealogical relationship evaluation of bacterial isolates with WGS data.
☆12Jan 17, 2022Updated 4 years ago
Alternatives and similar repositories for fast-GeP
Users that are interested in fast-GeP are comparing it to the libraries listed below
Sorting:
- Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data☆12Dec 17, 2025Updated last month
- Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.☆48Apr 2, 2025Updated 10 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆14Feb 2, 2025Updated last year
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- Long read metagenomics practical at EBAME18☆18Oct 3, 2018Updated 7 years ago
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- Fast and sensitive discovery of complete phages and prophages in bacterial genome sequences☆22Dec 16, 2024Updated last year
- whole genome MLST analysis☆52Jun 13, 2025Updated 8 months ago
- De novo VIral Genome Annotator☆24Jan 11, 2026Updated last month
- 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 last year
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆25Apr 24, 2018Updated 7 years ago
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆26Jan 30, 2025Updated last year
- YAMP: Yet Another Metagenomic Pipeline☆62Jun 5, 2023Updated 2 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 3 months ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Feb 6, 2025Updated last year
- Toolkit for preparing genomes for submission to NCBI☆29Sep 6, 2021Updated 4 years ago
- Haplotype-aware genome assembly toolkit☆30Jan 8, 2020Updated 6 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Jan 19, 2026Updated 3 weeks ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- ☆10May 14, 2025Updated 9 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.☆78Apr 16, 2025Updated 10 months ago
- The MLST pipeline developed by the PathOGiST research group☆36Nov 29, 2023Updated 2 years ago
- ☆10Jan 20, 2022Updated 4 years ago
- Automated pipeline for amplicon sequence analysis☆11Nov 25, 2025Updated 2 months ago
- Standardized and Automated MetaBarcoding Analyses workflow (Mirror)☆13Jun 28, 2023Updated 2 years ago
- Week 3 of the OSU CoMS Webinar: Introduction to Amplicon Sequencing (QIIME, DADA2, mothur) and Ecological Statistics☆10May 28, 2023Updated 2 years ago
- Learning the basics of reading and writing files in Python.☆10Mar 16, 2021Updated 4 years ago
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆91May 3, 2025Updated 9 months ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- ☆16Jan 30, 2026Updated 2 weeks ago
- GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.☆11Mar 22, 2024Updated last year
- ☆11Apr 5, 2021Updated 4 years ago
- Tutorial for Metagenomics Analyses☆10Jun 16, 2020Updated 5 years ago
- Pipeline to generate NGS reads from a phylogeny☆39Sep 13, 2022Updated 3 years ago
- tools for assessing the accuracy of genome assemblies☆35Apr 16, 2024Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆46Feb 5, 2026Updated last week