Illumina/BaseSpace_Clarity_LIMS

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18
Rank 1,208,065 (Top 24 %)
Language
Python
License
GNU General Publi...
Created over 7 years ago
Updated over 4 years ago

Illumina/BaseSpace_Clarity_LIMS

Illumina

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API libraries, application examples, and custom tools for BaseSpace Clarity LIMS

hap.py

Haplotype VCF comparison tools

manta

Structural variant and indel caller for mapped sequencing data

SpliceAI

A deep learning-based tool to identify splice variants

strelka

Strelka2 germline and somatic small variant caller

ExpansionHunter

A tool for estimating repeat sizes

Nirvana

The nimble & robust variant annotator

DRAGMAP

DRAGEN open-source mapper

paragraph

Graph realignment tools for structural variants

pyflow

A lightweight parallel task engine

canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data

PrimateAI

deep residual neural network for classifying the pathogenicity of missense mutations.

Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

PlatinumGenomes

The Platinum Genomes Truthset

ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

interop

C++ Library to parse Illumina InterOp files

REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats

akt

Ancestry and Kinship Tools

PrimateAI-3D

Polaris

Data and information about the Polaris study

SMNCopyNumberCaller

A copy number caller for SMN1 and SMN2 to enable SMA diagnosis and carrier screening with WGS

Cyrius

A tool to genotype CYP2D6 with WGS data

BeadArrayFiles

Python library to parse file formats related to Illumina bead arrays

GTCtoVCF

Script to convert GTC/BPM files to VCF

GraphAlignmentViewer

gvcfgenotyper

A utility for merging and genotyping Illumina-style GVCFs.

witty.er

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

isaac2

Aligner for sequencing data

Gauchian

A variant caller for the GBA gene using WGS data

Isaac3

Aligner for sequencing data

RepeatCatalogs

Isaac4

Isaac aligner version 4

happyR

R tools to interact with hap.py output

agg

gvcf aggregation tool

tHapMix

Haplotype-based somatic genome simulator

happyCompare

Reporting toolbox for happy output

zippy

The ZIPPY pipeline prototyping system

MarViN

ica-sdk-python

NirvanaDocumentation

novaseq-lims-api

Documentation and tools for users of the NovaSeq LIMS API

NeoMutalyzer

Inspired by Mutalyzer and frustrated by RefSeq, we created this transcript annotation validator

dragen-azure-quickstart

Pelops

licenses

BlockCompression

Block compression library used by Nirvana

dragen-aws-batch-quickstart