Illumina

Repositories

• ExpansionHunter

  A tool for estimating repeat sizes
  C++ 16 81 15 1 Updated Dec 20, 2020

• interop

  C++ Library to parse Illumina InterOp files

  python csharp cpp python3 interop swig python27
  C++ GPL-3.0 19 53 1 1 Updated Dec 19, 2020

• NirvanaDocumentation
  JavaScript 0 0 0 0 Updated Dec 17, 2020

• REViewer

  A tool for visualizing alignments of reads in regions containing tandem repeats
  C++ 0 8 0 0 Updated Dec 17, 2020

• Cyrius

  A tool to genotype CYP2D6 with WGS data

  wgs pharmacogenomics cyp2d6
  Python Apache-2.0 3 17 4 0 Updated Dec 16, 2020

• witty.er

  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

  benchmarking variants cnv copy-number-variation variant-analysis structural-variation
  C# 1 15 1 0 Updated Dec 10, 2020

• SpliceAI

  A deep learning-based tool to identify splice variants
  Python 62 156 1 1 Updated Dec 9, 2020

• SMNCopyNumberCaller

  A copy number caller for SMN1 and SMN2 to enable SMA diagnosis and carrier screening with WGS
  Python 5 22 0 0 Updated Dec 2, 2020

• Nirvana

  The nimble & robust variant annotator
  C# GPL-3.0 22 96 10 1 Updated Nov 20, 2020

• BeadArrayFiles

  Python library to parse file formats related to Illumina bead arrays
  Python 22 29 7 1 Updated Oct 28, 2020

• strelka

  Strelka2 germline and somatic small variant caller

  bioinformatics snps indels snvs
  C++ 69 230 82 3 Updated Oct 16, 2020

• ExpansionHunterDenovo

  A suite of tools for detecting expansions of short tandem repeats
  C++ 9 29 11 0 Updated Aug 26, 2020

• GTCtoVCF

  Script to convert GTC/BPM files to VCF
  Python Apache-2.0 19 24 10 1 Updated Jul 9, 2020

• BaseSpace_Clarity_LIMS

  API libraries, application examples, and custom tools for BaseSpace Clarity LIMS
  Python GPL-3.0 6 14 1 2 Updated Jul 3, 2020

• pyflow

  A lightweight parallel task engine

  workflow workflow-engine task-runner
  Python 35 105 13 0 Updated Jul 1, 2020

• Isaac4

  Isaac aligner version 4
  C++ 4 12 2 0 Updated Jun 19, 2020

• GraphAlignmentViewer
  Python 4 20 1 0 Updated Jun 5, 2020

• akt

  Ancestry and Kinship Tools
  C++ GPL-3.0 9 47 3 1 Updated May 22, 2020

• hap.py

  Haplotype VCF comparison tools

  bioinformatics genomics vcf vcf-comparison
  C++ 77 240 67 2 Updated Feb 27, 2020

• Polaris

  Data and information about the Polaris study
  6 31 5 0 Updated Nov 18, 2019

• paragraph

  Graph realignment tools for structural variants

  vcf variant-calling htslib structural-variation genotyping
  C++ Apache-2.0 16 92 12 0 Updated Sep 24, 2019

• canvas Archived

  Canvas - Copy number variant (CNV) calling from DNA sequencing data
  C# 17 108 40 0 Updated Sep 3, 2019

• zippy

  The ZIPPY pipeline prototyping system

  python workflow bioinformatics pipeline
  Python Apache-2.0 4 5 1 0 Updated Aug 15, 2019

• Pisces

  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  C# 13 67 38 0 Updated Aug 9, 2019

• manta

  Structural variant and indel caller for mapped sequencing data

  bioinformatics structural-variations indels structural-variation
  C++ 81 252 78 0 Updated Jul 17, 2019

• happyR

  R tools to interact with hap.py output

  bioinformatics r variant-analysis vcf-comparison
  R BSD-3-Clause 1 11 0 0 Updated Jul 12, 2019

• happyCompare Archived

  Reporting toolbox for happy output

  benchmarking bioinformatics r variant-analysis
  R 4 7 0 0 Updated Jul 12, 2019

• novaseq-lims-api

  Documentation and tools for users of the NovaSeq LIMS API
  C# 1 2 0 0 Updated Mar 14, 2019

• PrimateAI

  deep residual neural network for classifying the pathogenicity of missense mutations.
  Python 22 62 5 0 Updated Feb 26, 2019

• gvcfgenotyper

  A utility for merging and genotyping Illumina-style GVCFs.
  C++ Apache-2.0 2 25 2 0 Updated Feb 26, 2019