IS mapping software
☆57Dec 3, 2021Updated 4 years ago
Alternatives and similar repositories for IS_mapper
Users that are interested in IS_mapper are comparing it to the libraries listed below
Sorting:
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Jul 30, 2024Updated last year
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 4 years ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆105Dec 5, 2025Updated 2 months ago
- Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram☆12Aug 20, 2024Updated last year
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…☆73Oct 6, 2020Updated 5 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- ☆38Apr 14, 2022Updated 3 years ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- Plasmid exploration of bacterial genomes☆23Mar 2, 2022Updated 4 years ago
- SEER, reimplemented in python 🐍🔮☆131May 22, 2025Updated 9 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
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆95Dec 9, 2025Updated 2 months ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- panISa is a software to search insertion sequence (IS) on resequencing data (bam file)☆24Apr 11, 2024Updated last year
- Pneumococcal Capsular Typing tool for NGS data☆18Apr 6, 2021Updated 4 years ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆168Apr 16, 2025Updated 10 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- A script for comparing old vs new versions of genome annotations☆21Aug 1, 2023Updated 2 years ago
- ☆59Feb 23, 2026Updated last week
- Recombination-free trees☆63Sep 1, 2025Updated 6 months ago
- "Reads to report" for public health and clinical microbiology☆143Dec 9, 2025Updated 2 months ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Apr 16, 2024Updated last year
- hybrid assembly pipeline for bacterial genomes☆634Jul 25, 2024Updated last year
- Making whole bacterial genome sequencing data analysis easy☆114Apr 22, 2025Updated 10 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Split Kmer Analysis☆66May 26, 2022Updated 3 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- in silico typing of the H. influenzae cap locus☆12Jul 15, 2024Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated last year
- This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data☆12Dec 1, 2025Updated 3 months ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated last year
- GenoVi, an automated customizable circular genome visualizer for bacteria and archaea☆103Jun 25, 2023Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21May 16, 2023Updated 2 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆44Aug 20, 2025Updated 6 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆104Feb 9, 2026Updated 3 weeks ago