elPrep: a high-performance tool for analyzing sequence alignment/map files in sequencing pipelines.
☆292Jun 2, 2023Updated 2 years ago
Alternatives and similar repositories for elprep
Users that are interested in elprep are comparing it to the libraries listed below
Sorting:
- biogo high throughput sequencing repository☆133Aug 28, 2025Updated 6 months ago
- elPrep reimplementations in C++ and Java, only for benchmark comparisons☆10Feb 13, 2023Updated 3 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- The next version of bwa-mem☆824Oct 15, 2025Updated 5 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆334May 27, 2025Updated 9 months ago
- Tools for early stage alignment file processing☆95Mar 12, 2019Updated 7 years ago
- Structural variant detection and association testing☆108Feb 2, 2023Updated 3 years ago
- Toolkit for calling structural variants using short or long reads☆115Mar 7, 2026Updated 2 weeks ago
- lumpy: a general probabilistic framework for structural variant discovery☆338Feb 22, 2026Updated 3 weeks ago
- Tools for working with SAM/BAM data☆606Dec 22, 2024Updated last year
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- Long read aligner☆114May 26, 2023Updated 2 years ago
- Robust individual and aggregate checksums for nucleotide sequences☆17Mar 3, 2026Updated 2 weeks ago
- URMAP ultra-fast read mapper☆38Jun 15, 2020Updated 5 years ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆399Aug 30, 2025Updated 6 months ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 6 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- ☆286Dec 29, 2025Updated 2 months ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 3 months ago
- elPrep: a high-performance tool for preparing sequencing alignment/map files in sequencing pipelines (Lisp version)☆14Feb 22, 2019Updated 7 years ago
- Graph realignment tools for structural variants☆166Dec 8, 2022Updated 3 years ago
- ABRA2☆95Dec 2, 2022Updated 3 years ago
- Quickly calculate and visualize sequence coverage in alignment files☆100Jun 22, 2019Updated 6 years ago
- VariantStore: A Large-Scale Genomic Variant Search Index☆39Jul 9, 2021Updated 4 years ago
- Bioinformatic infrastructure libraries☆78Aug 18, 2020Updated 5 years ago
- Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang☆31Apr 20, 2020Updated 5 years ago
- Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang☆47Jul 12, 2020Updated 5 years ago
- Parallel Recipes : parallel workflow execution made easy☆13Sep 1, 2015Updated 10 years ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 4 years ago
- A read extraction and realignment tool for next generation sequencing data☆105Oct 29, 2022Updated 3 years ago
- ☆13Jan 23, 2020Updated 6 years ago
- Strelka2 germline and somatic small variant caller☆391Dec 29, 2021Updated 4 years ago
- Genome browser and variant annotation☆392Oct 30, 2025Updated 4 months ago
- Flexible genotype query among 30,000+ samples whole-genome☆94Sep 4, 2019Updated 6 years ago
- New url: https://github.com/biointec/halvade☆19Apr 19, 2017Updated 8 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 11 months ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated last month
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- ☆33Aug 2, 2022Updated 3 years ago