breseq is a computational pipeline for finding mutations relative to a reference sequence using high-throughput DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++.
☆213Sep 20, 2026Updated this week
Alternatives and similar repositories for breseq
Users that are interested in breseq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reorients assembled microbial sequences☆146Jun 30, 2026Updated 2 months ago
- Genomics resources for the Long-Term Evolution Experiment with E. coli☆20Jul 11, 2026Updated 2 months ago
- Rapid haploid variant calling and core genome alignment☆593Dec 12, 2025Updated 9 months ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆156Jun 10, 2026Updated 3 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆239Sep 17, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- IS mapping software☆59Dec 3, 2021Updated 4 years ago
- An updated pipeline for pangenome investigation☆377Jul 2, 2026Updated 2 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆681Aug 7, 2026Updated last month
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆48Sep 9, 2026Updated 2 weeks ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆348Jul 24, 2026Updated 2 months ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Dec 4, 2018Updated 7 years ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆91Sep 9, 2026Updated 2 weeks ago
- wrangling and model-free analysis of microbial growth curve data in R with gcplyr☆39May 8, 2026Updated 4 months ago
- Rapid prokaryotic genome annotation☆995Jan 6, 2026Updated 8 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- hybrid assembly pipeline for bacterial genomes☆653Jul 29, 2026Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆66Jun 16, 2025Updated last year
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆158Sep 2, 2026Updated 3 weeks ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆268Jun 11, 2026Updated 3 months ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆183Aug 10, 2026Updated last month
- Bacterial GWAS analysis☆58Jun 12, 2026Updated 3 months ago
- a short-read polishing tool for long-read assemblies☆226Jul 28, 2026Updated last month
- Build a partitioned pangenome graph from microbial genomes☆313Updated this week
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆133Feb 26, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Create a tree using Mash distances☆190Oct 24, 2023Updated 2 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆47Sep 3, 2020Updated 6 years ago
- A flexible pipeline for complete analysis of bacterial genomes☆522Aug 5, 2026Updated last month
- NCBI Prokaryotic Genome Annotation Pipeline☆390Aug 19, 2026Updated last month
- SKESA assembler☆127Oct 11, 2024Updated last year
- Pan-genome wide association studies☆226May 29, 2024Updated 2 years ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆264May 13, 2026Updated 4 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆72Apr 10, 2025Updated last year
- Bifrost graph gene caller.☆101Aug 31, 2026Updated 3 weeks 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.
- Application and Python module for average nucleotide identity analyses of microbes.☆218Jul 1, 2025Updated last year
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆10Jun 13, 2023Updated 3 years ago
- Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.☆231Sep 17, 2026Updated last week
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆131Oct 30, 2023Updated 2 years ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆116Dec 5, 2025Updated 9 months ago
- Plasmid analysis using rearrangement distances☆56Jul 19, 2026Updated 2 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆208Jun 10, 2026Updated 3 months ago