Alternatives and similar repositories for bwa:

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

• quim0 / WFA-GPU
  GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
  ☆31Updated 4 months ago
• gsneha26 / SegAlign
  A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043
  ☆67Updated 6 months ago
• NVIDIA / VariantWorks
  Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
  ☆45Updated 2 years ago
• yukiteruono / pbsim2
  PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
  ☆71Updated last year
• kaist-ina / BWA-MEME
  BWA-MEME: Faster BWA-MEM2 using learned-index
  ☆116Updated 7 months ago
• WGLab / NanoCaller
  Variant calling tool for long-read sequencing data
  ☆104Updated 3 weeks ago
• human-pangenomics / HPP_Year1_Assemblies
  Assemblies from HPP Year 1 production
  ☆71Updated last year
• comprna / RATTLE
  Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
  ☆57Updated last year
• human-pangenomics / hpp_pangenome_resources
  ☆104Updated last year
• HKU-BAL / ClairS
  ClairS - a deep-learning method for long-read somatic small variant calling
  ☆79Updated 2 months ago
• stat-lab / EvalSVcallers
  Evaluate the performances (precision and recall) of structural variation (SV) callers
  ☆34Updated 4 months ago
• human-pangenomics / HG002_Data_Freeze_v1.0
  Human Pangenome Reference Consortium - HG002 Data Freeze (v1.0)
  ☆76Updated 2 years ago
• ruanjue / bsalign
  Banded Striped DNA Sequence Alignment
  ☆45Updated last year
• jzook / genome-data-integration
  Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls
  ☆43Updated 3 years ago
• genome-in-a-bottle / genome-stratifications
  Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium…
  ☆78Updated 2 years ago
• zhangwei2015 / IMonitor
  This script use to analyze the immune repertoire sequenced by high throughtput sequencing
  ☆24Updated 3 years ago
• TheJacksonLaboratory / Picky
  Structural Variants Pipeline for Long Reads
  ☆44Updated 6 years ago
• PopicLab / cue
  Deep learning framework for SV calling and genotyping
  ☆104Updated last year
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆73Updated 5 years ago
• EIHealth-Lab / fast-bonito
  ☆25Updated 4 years ago
• hasindu2008 / slow5tools
  Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
  ☆96Updated this week
• HKU-BAL / ClairS-TO
  ClairS-TO - a deep-learning method for tumor-only somatic variant calling
  ☆58Updated 2 months ago
• vgteam / graph-genomics-review
  Pangenome graphs (review article on graph-based pangenomic methods)
  ☆71Updated 4 years ago
• Sentieon / sentieon-scripts
  Helper scripts for biological data processing from Sentieon
  ☆63Updated 3 months ago
• gymreklab / GangSTR
  A tool for profiling long STRs from short reads
  ☆94Updated 3 years ago
• human-pangenomics / hpgp-data
  Data from the Human PanGenomics Project
  ☆60Updated 3 years ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆51Updated 8 months ago
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated 9 months ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆39Updated last month
• zichner / primerDesign
  A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants
  ☆45Updated 7 years ago