Pinned Repositories
canvas
Canvas - Copy number variant (CNV) calling from DNA sequencing data
DRAGMAP
DRAGEN open-source mapper
ExpansionHunter
A tool for estimating repeat sizes
hap.py
Haplotype VCF comparison tools
manta
Structural variant and indel caller for mapped sequencing data
Nirvana
The nimble & robust variant annotator
paragraph
Graph realignment tools for structural variants
pyflow
A lightweight parallel task engine
SpliceAI
A deep learning-based tool to identify splice variants
strelka
Strelka2 germline and somatic small variant caller
Illumina's Repositories
Illumina/strelka
Strelka2 germline and somatic small variant caller
Illumina/pyflow
A lightweight parallel task engine
Illumina/canvas
Canvas - Copy number variant (CNV) calling from DNA sequencing data
Illumina/PrimateAI
deep residual neural network for classifying the pathogenicity of missense mutations.
Illumina/Pisces
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
Illumina/PlatinumGenomes
The Platinum Genomes Truthset
Illumina/Polaris
Data and information about the Polaris study
Illumina/GraphAlignmentViewer
Illumina/gvcfgenotyper
A utility for merging and genotyping Illumina-style GVCFs.
Illumina/isaac2
Aligner for sequencing data
Illumina/RepeatCatalogs
Illumina/BaseSpace_Clarity_LIMS
API libraries, application examples, and custom tools for BaseSpace Clarity LIMS
Illumina/Isaac3
Aligner for sequencing data
Illumina/Isaac4
Isaac aligner version 4
Illumina/happyR
R tools to interact with hap.py output
Illumina/agg
gvcf aggregation tool
Illumina/tHapMix
Haplotype-based somatic genome simulator
Illumina/happyCompare
Reporting toolbox for happy output
Illumina/MarViN
Illumina/NeoMutalyzer
Inspired by Mutalyzer and frustrated by RefSeq, we created this transcript annotation validator
Illumina/BlockCompression
Block compression library used by Nirvana
Illumina/BamMetrics
Efficient and accurate metrics from aligned reads - mismatch rate, percent proper pairs, etc.
Illumina/CacheUtils
Creates new Nirvana gene & transcript cache files
Illumina/GffCreator
Creates GFF files from Nirvana cache files
Illumina/SlimCache
Nirvana tool that creates RefSeq- or Ensembl-specific cache files