Numerical Encoding for Human Genetic Variants
☆42Jun 8, 2023Updated 2 years ago
Alternatives and similar repositories for variantkey
Users that are interested in variantkey are comparing it to the libraries listed below
Sorting:
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Dec 3, 2017Updated 8 years ago
- Linear-time, low-memory construction of variation graphs☆20Feb 3, 2020Updated 6 years ago
- Stupid Simple (ba)Sh Testing - A functional software testing framwork☆23Nov 8, 2023Updated 2 years ago
- Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point f…☆11Dec 11, 2020Updated 5 years ago
- Graphite - Graph-based variant adjudication☆28Feb 9, 2021Updated 5 years ago
- VEP-like tool for sequence ontology and HGVS annotation of VCF files☆27Mar 9, 2026Updated last week
- Software for error-tolerant coding of information into DNA sequences using finite-state transducers.☆12Jan 8, 2017Updated 9 years ago
- AlignerBoost is a generalized software toolkit for boosting Next-Gen sequencing mapping precision using a Bayesian based mapping quality …☆11Mar 1, 2022Updated 4 years ago
- A fast Python library for VCF files leveraging Cython for speed.☆52Mar 27, 2018Updated 7 years ago
- C++ htslib/bwa-mem/fermi interface for interrogating sequence data☆138Sep 16, 2025Updated 6 months ago
- Implicit Interval Tree with Interpolation Index☆42Jul 13, 2022Updated 3 years ago
- pathoscore evaluates variant pathogenicity tools and scores.☆22Mar 25, 2022Updated 3 years ago
- The python binding for D4 format☆16Oct 22, 2021Updated 4 years ago
- horizontal pileup☆16Nov 11, 2022Updated 3 years ago
- ☆15Aug 14, 2020Updated 5 years ago
- Building the constrained coding regions (CCR) model☆16Dec 19, 2018Updated 7 years ago
- Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently☆59Oct 29, 2023Updated 2 years ago
- A collection of CSV/TSV Utilities☆13Jun 2, 2020Updated 5 years ago
- High-level API for storing and querying sequence variant data☆20May 24, 2019Updated 6 years ago
- Command line tools for IntSpan related bioinformatics operations☆12Apr 9, 2025Updated 11 months ago
- ☆24Feb 16, 2026Updated last month
- Index and query k-mer matrices in BGZF☆12Apr 30, 2018Updated 7 years ago
- [IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long read…☆125Sep 10, 2018Updated 7 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- A succinct colored dBG representation☆12Sep 11, 2018Updated 7 years ago
- A lightweight Python graphing API for genomic features☆15Jul 8, 2022Updated 3 years ago
- using all the bits for echt rapid variant annotation and filtering☆154Feb 18, 2026Updated last month
- A Rust library for storing generic genomic data by sorted chromosome name☆17Sep 26, 2024Updated last year
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Toolkit for extracting SVs from long sequences and benchmarking variant callers☆13Jan 10, 2017Updated 9 years ago
- use the noise☆15Apr 15, 2020Updated 5 years ago
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Dec 16, 2019Updated 6 years ago
- DNA kmer operations for nim☆14Apr 24, 2022Updated 3 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- Integrated Variant Caller☆17Mar 15, 2018Updated 8 years ago
- fast easy interval overlapping for nim-lang☆29Jul 9, 2025Updated 8 months ago
- Population-based detection of structural variation from High-Throughput Sequencing.☆33Aug 9, 2022Updated 3 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- reference free variant assembly☆34Jul 14, 2023Updated 2 years ago