lh3 / cgrangesLinks
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
☆169Updated last year
Alternatives and similar repositories for cgranges
Users that are interested in cgranges are comparing it to the libraries listed below
Sorting:
- Code examples of fast and simple k-mer counters for tutorial purposes☆170Updated 5 years ago
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆221Updated last month
- C++ htslib/bwa-mem/fermi interface for interrogating sequence data☆138Updated 2 months ago
- A fast K-mer counter for high-fidelity shotgun datasets☆135Updated 3 months ago
- Find all significant local alignments between reads☆141Updated last year
- SIMD partial order alignment tool/library☆170Updated 2 months ago
- Genotype and phase short tandem repeats using Illumina whole-genome sequencing data☆101Updated 2 years ago
- A fast approximate aligner for long DNA sequences☆284Updated last year
- An efficient index for the colored, compacted, de Bruijn graph☆110Updated last year
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆131Updated 2 months ago
- Graphical Fragment Assembly (GFA) Format Specification☆217Updated last year
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Updated 5 years ago
- An efficient FASTQ manipulation suite☆138Updated 5 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆142Updated 3 months ago
- Global alignment and alignment extension☆139Updated 2 years ago
- Small utilities for working with fastq sequence files.☆123Updated 3 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated 9 months ago
- alignment to variation graph inducer☆152Updated this week
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆242Updated last year
- Implementation of Positional Burrows-Wheeler Transform for genetic data☆112Updated 3 weeks ago
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆134Updated last month
- Long read aligner☆115Updated 2 years ago
- ABRA2☆95Updated 3 years ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Updated 3 years ago
- LoFreq Star: Sensitive variant calling from sequencing data☆108Updated last month
- De novo genome assembly and multisample variant calling☆112Updated 6 years ago
- Fast multi-line FASTA/Q reader in several programming languages☆176Updated 4 years ago
- FASTQ compression☆140Updated 2 years ago
- A repository for generating strobemers and evalaution☆79Updated last year
- AdapterRemoval v2 - rapid adapter trimming, identification, and read merging☆113Updated last week