deepBreaks , a computational method, aims to identify important changes in association with the phenotype of interest using multi-alignment sequencing data from a population.
☆12Oct 22, 2025Updated 4 months ago
Alternatives and similar repositories for deepbreaks
Users that are interested in deepbreaks are comparing it to the libraries listed below
Sorting:
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Phasing of dikaryotic fungal genome assemblies☆13Mar 1, 2023Updated 3 years ago
- ☆16Jan 14, 2026Updated last month
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 4 months ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 8 months ago
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- ☆14Sep 11, 2023Updated 2 years ago
- Generating UTRs from SHort Reads☆11Sep 28, 2020Updated 5 years ago
- ☆17Feb 11, 2026Updated 3 weeks ago
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆32Jan 3, 2022Updated 4 years ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆19Feb 24, 2026Updated last week
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago
- ☆21Jan 13, 2026Updated last month
- A plant organellar Graphical Fragment Assembly toolkit☆16Sep 10, 2025Updated 5 months ago
- ☆22Feb 10, 2026Updated 3 weeks ago
- Centromere mapping and annotation pipeline☆23Updated this week
- PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.☆18Feb 26, 2026Updated last week
- ☆19Feb 15, 2025Updated last year
- A Nextflow pipeline for running synteny analysis.☆16Jun 17, 2025Updated 8 months ago
- Efficient retrieval, download, and unification of genomic data from leading biodiversity databases☆18Updated this week
- A nextflow pipeline for polishing CLR assemblies☆18Feb 3, 2023Updated 3 years ago
- a programme for visualization of short sequence alignment and path navigation in graphical pan-genome☆26Jan 23, 2024Updated 2 years ago
- Genotyping of copy number sensitive allele-specific haplotypes☆27Nov 6, 2025Updated 3 months ago
- ☆18Jan 29, 2025Updated last year
- Phasing reads with secondary alignments☆22Nov 30, 2024Updated last year
- A tool for quick and accurate calculation of syntenic diversity.☆42Sep 22, 2025Updated 5 months ago
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆23Feb 16, 2026Updated 2 weeks ago
- Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.☆20Feb 13, 2026Updated 2 weeks ago
- Toolkit for manipulating FASTA and SAM files☆23Mar 14, 2024Updated last year
- COsine SImilarity-based Genotyper using pangenomes☆31Feb 13, 2026Updated 2 weeks ago
- A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…☆27Feb 23, 2026Updated last week
- Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis☆24Dec 15, 2025Updated 2 months ago
- Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.☆26Updated this week
- Extracts subgraphs or components from a graph in GFA format☆24Nov 18, 2024Updated last year
- A web-based, interactive pangenome visualization tool☆21Apr 10, 2023Updated 2 years ago
- Gene Ontology subgraph visualizations☆20Jan 6, 2026Updated last month
- ☆20Dec 13, 2023Updated 2 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 6 months ago
- Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.☆26Oct 24, 2025Updated 4 months ago