Alternatives and similar repositories for GKL:

Users that are interested in GKL are comparing it to the libraries listed below

• lh3 / ksw2
  Global alignment and alignment extension
  ☆130Updated last year
• Intel-HLS / GenomicsDB
  GenomicsDB
  ☆111Updated 2 years ago
• ytchen0323 / cloud-scale-bwamem
  ☆15Updated 7 years ago
• lh3 / minimap
  This repo is DEPRECATED. Please use minimap2, the successor of minimap.
  ☆105Updated 7 years ago
• broadgsa / gatk-protected
  Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinst…
  ☆143Updated 6 years ago
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆137Updated 5 months ago
• smarco / WFA-paper
  Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
  ☆201Updated 2 years ago
• smarco / WFA2-lib
  WFA-lib: Wavefront alignment algorithm library v2
  ☆164Updated this week
• pangenome / odgi
  Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
  ☆198Updated last week
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆96Updated last month
• sequencing / isaac_variant_caller
  This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka
  ☆38Updated 7 years ago
• thegenemyers / DALIGNER
  Find all significant local alignments between reads
  ☆140Updated 6 months ago
• MauricioCarneiro / PairHMM
  Optimization of a Haplotype PairHMM class for GPU processing
  ☆24Updated 7 years ago
• UCLA-VAST / minimap2-acceleration
  Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository
  ☆33Updated 2 months ago
• jeffdaily / parasail
  Pairwise Sequence Alignment Library
  ☆246Updated last year
• citiususc / SparkBWA
  SparkBWA is a new tool that exploits the capabilities of a Big Data technology as Apache Spark to boost the performance of one of the mos…
  ☆69Updated 5 years ago
• ocxtal / minialign
  [IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long read…
  ☆126Updated 6 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• richarddurbin / pbwt
  Implementation of Positional Burrows-Wheeler Transform for genetic data
  ☆102Updated last month
• enasequence / cramtools
  CRAM format specification and java API for read data.
  ☆58Updated 6 years ago
• GenomicsDB / GenomicsDB
  High performance data storage for importing, querying and transforming variants.
  ☆97Updated 3 weeks ago
• refresh-bio / KMC
  Fast and frugal disk based k-mer counter
  ☆281Updated last month
• rvaser / spoa
  SIMD partial order alignment tool/library
  ☆163Updated last year
• Illumina / PlatinumGenomes
  The Platinum Genomes Truthset
  ☆85Updated 7 years ago
• minhhpham / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆16Updated last year
• ocxtal / libgaba
  Adaptive semi-global banded alignment on string graphs
  ☆65Updated 6 years ago
• PacificBiosciences / FALCON-integrate
  Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
  ☆31Updated 6 years ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆73Updated 5 years ago
• PASSIONLab / BELLA
  BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
  ☆48Updated 2 years ago
• lh3 / kmer-cnt
  Code examples of fast and simple k-mer counters for tutorial purposes
  ☆167Updated 4 years ago