lumpy: a general probabilistic framework for structural variant discovery
☆338Feb 22, 2026Updated last week
Alternatives and similar repositories for lumpy-sv
Users that are interested in lumpy-sv are comparing it to the libraries listed below
Sorting:
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆507Nov 6, 2025Updated 3 months ago
- Structural variant and indel caller for mapped sequencing data☆458Oct 11, 2025Updated 4 months ago
- Bayesian genotyper for structural variants☆136Mar 6, 2021Updated 4 years ago
- Structural variation and indel detection by local assembly☆252Sep 16, 2025Updated 5 months ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆264Jun 17, 2024Updated last year
- A flexible framework for rapid genome analysis and interpretation☆319Oct 18, 2022Updated 3 years ago
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆233Feb 17, 2022Updated 4 years ago
- Toolset for SV simulation, comparison and filtering☆411Dec 1, 2023Updated 2 years ago
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆176Jan 7, 2020Updated 6 years ago
- Structural variant detection and association testing☆108Feb 2, 2023Updated 3 years ago
- Structural variation caller using third generation sequencing☆636Dec 18, 2025Updated 2 months ago
- Plot structural variant signals from many BAMs and CRAMs☆558Jul 13, 2024Updated last year
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆279May 21, 2025Updated 9 months ago
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆175Aug 22, 2024Updated last year
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- Tools for processing and analyzing structural variants.☆157May 2, 2022Updated 3 years ago
- Jasmine: SV Merging Across Samples☆241Dec 20, 2024Updated last year
- Long read based human genomic structural variation detection with cuteSV☆277Sep 30, 2025Updated 5 months ago
- Structural variant toolkit for VCFs☆397Jan 23, 2026Updated last month
- Annotation and Ranking of Structural Variation☆287Oct 7, 2025Updated 4 months ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆864Feb 8, 2026Updated 3 weeks ago
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆307Mar 18, 2024Updated last year
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆668Oct 31, 2025Updated 4 months ago
- Strelka2 germline and somatic small variant caller☆390Dec 29, 2021Updated 4 years ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- Population-scale genotyping using pangenome graphs☆196Jan 9, 2025Updated last year
- Graph realignment tools for structural variants☆165Dec 8, 2022Updated 3 years ago
- SV detection from paired end reads mapping☆118Jul 31, 2019Updated 6 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆826Feb 10, 2026Updated 2 weeks ago
- The next version of bwa-mem☆819Oct 15, 2025Updated 4 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆334May 27, 2025Updated 9 months ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆59Jun 30, 2017Updated 8 years ago
- TIDDIT - structural variant calling☆78Dec 8, 2025Updated 2 months ago
- ☆51Aug 27, 2019Updated 6 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- Copy number variant detection from targeted DNA sequencing☆602Updated this week
- Sequence-to-graph mapper and graph generator☆470Aug 11, 2025Updated 6 months ago
- a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads☆211Oct 2, 2025Updated 5 months ago