tseemann / berokkaView external linksLinks
🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
☆24Sep 7, 2019Updated 6 years ago
Alternatives and similar repositories for berokka
Users that are interested in berokka are comparing it to the libraries listed below
Sorting:
- Assembly based core genome SNP alignments for bacteria☆25Oct 23, 2019Updated 6 years ago
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆22May 8, 2024Updated last year
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 6 years ago
- Tool for visualising assemblies.☆17Sep 15, 2015Updated 10 years ago
- Pipeline for Evaluating Prokaryotic References☆11Sep 16, 2016Updated 9 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Jan 14, 2026Updated last month
- Tool (experimental) to compute layout from overlaps with spectral algorithm☆11Nov 28, 2017Updated 8 years ago
- The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)☆17Oct 12, 2018Updated 7 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- reference-based long read assemblies of bacterial genomes☆51Aug 9, 2021Updated 4 years ago
- scripts to parse IrysView output☆11Jun 24, 2015Updated 10 years ago
- Luslab nextflow modules☆14Apr 30, 2021Updated 4 years ago
- Pan-genome wide association studies☆207May 29, 2024Updated last year
- Pairwise SNP distance matrix from a FASTA sequence alignment☆151Dec 31, 2025Updated last month
- Variant call verification☆16May 12, 2025Updated 9 months ago
- ☆15Jun 27, 2024Updated last year
- A fast tool for hybrid genome assembly of long and short reads☆78Apr 22, 2020Updated 5 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆339Sep 11, 2025Updated 5 months ago
- A simple toolkit for manipulating nanopore signal data☆19Sep 24, 2024Updated last year
- CRyPTIC data processing pipelines☆34Jul 18, 2024Updated last year
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads☆67Nov 4, 2021Updated 4 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago
- Rapid determination of appropriate reference genomes.☆99Jan 22, 2025Updated last year
- Correcting errors in noisy long reads using variation graphs☆50Nov 17, 2022Updated 3 years ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆79Nov 23, 2023Updated 2 years ago
- Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"☆64Oct 15, 2020Updated 5 years ago
- Making whole bacterial genome sequencing data analysis easy☆114Apr 22, 2025Updated 9 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆94Dec 9, 2025Updated 2 months ago
- A list of weak Bacterial assemblies in GenBank☆18Aug 3, 2017Updated 8 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Apr 1, 2025Updated 10 months ago
- Genome size estimation from long read overlaps☆80Dec 1, 2025Updated 2 months ago
- A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.☆90Nov 23, 2024Updated last year
- MetaCompass: Reference-guided Assembly of Metagenomes☆43Aug 13, 2025Updated 6 months ago
- A Python library for reading and writing PacBio® data files☆41Dec 11, 2025Updated 2 months ago
- 🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations☆35May 21, 2024Updated last year
- 🪡Correct and scaffold assemblies using long reads☆57Sep 4, 2025Updated 5 months ago
- ☆18Nov 16, 2015Updated 10 years ago