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Search results for variants sequencing

6 search results found

Deepvariant ⭐ 2,978

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Copy number variant detection from targeted DNA sequencing

Sequence correction provided by ONT Research

Structural variant and indel caller for mapped sequencing data

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Alignment And Variant Calling Tutorial ⭐ 192

basic walk-throughs for alignment and variant calling from NGS sequencing data

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Dna Seq Analysis ⭐ 128

DNA sequencing analysis notes from Ming Tang

Dragonstar2019 ⭐ 122

Gatk4 Data Processing ⭐ 99

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

Ngs Pipe ⭐ 87

NGS-pipe: next-generation sequencing pipelines for precision oncology

LoFreq Star: Sensitive variant calling from sequencing data

Parliament2 ⭐ 83

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Scalable gVCF merging and joint variant calling for population sequencing projects

Sv Cnv Studies ⭐ 81

📚 Relevant papers for CNV and SV approaches

Phylowgs ⭐ 78

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

Nanocaller ⭐ 78

Variant calling tool for long-read sequencing data

Variantbam ⭐ 71

Filtering and profiling of next-generational sequencing data using region-specific rules

xHLA: Fast and accurate HLA typing from short read sequence data

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Svim Asm ⭐ 48

Structural Variant Identification Method using Genome Assemblies

Sv Plaudit ⭐ 47

Pipeline for structural variant image curation and analysis.

Exomedepth ⭐ 46

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

Platinumgenomes ⭐ 42

The Platinum Genomes Truthset

Rtg Core ⭐ 41

RTG Core: Software for alignment and analysis of next-gen sequencing data.

Ngsepcore ⭐ 40

NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).

Needlestack ⭐ 39

Multi-sample somatic variant caller

10x Genomics Reads Simulator

Isaac_variant_caller ⭐ 38

This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka

Gatk4 Exome Analysis Pipeline ⭐ 37

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

Structural variant caller for low-depth long-read sequencing data

Genome Data Integration ⭐ 35

Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls

Phenopolis ⭐ 32

An Open Platform for Harmonisation & Analysis of Sequencing & Phenotype Data

Bio Dockers ⭐ 32

🐳 Bio-dockers: dockerized bioinformatic tools

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Seqminer ⭐ 28

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

Varianttools ⭐ 27

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis

Ngs Filters ⭐ 25

Filters for false-positive mutation calls in NGS

Error correction and variant calling algorithm for nanopore sequencing

Variant Filter ⭐ 25

A false-positive filter for variants called from massively parallel sequencing

Giab_tools_methods ⭐ 22

This repository contains a list of tools or methods that have been used in GIAB analysis

PathOS is a clinical application for filtering, analysing and reporting on NGS variants

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples

Tool to find regions of homozygosity (ROHs) from sequencing data.

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

Roslin Variant ⭐ 15

Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis

A support vector machine for calling variants from next-gen sequencing data

Clinicalgradednaseq ⭐ 15

Automated next generation DNA sequencing analysis pipeline suited for clinical tests, with >99.9% sensitivity to Sanger sequencing at read-depth>18

Miracum Pipe ⭐ 14

Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.

NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC

Variantbam ⭐ 13

Filtering and profiling of next-generational sequencing data using region-specific rules

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr

Quasimodo ⭐ 12

QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

Pyseqarray ⭐ 12

PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)

CAVA (Clinical Annotation of VAriants)

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Deepvariant On Spark ⭐ 11

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

Cruk Summer School 2017 ⭐ 11

Analysis of Cancer Genomes; 2017 edition

Lolopicker ⭐ 10

picking up low allelic-fraction, somatic variants from tumor samples

Detect and phase minor SNVs from long-read sequencing data

Simulate next-generation sequencing reads for tumor samples

Pdx_exomeseq ⭐ 9

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

FLT3 ITD detection (ITDseek) and simulation (ITDsim)

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Breakpointer ⭐ 8

Breakpointer is a fast algorithm to locate breakpoints of structural variants from single-end reads produced by next-generation sequencing.

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

Multibreak Sv ⭐ 7

MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

map and call next generation genomic sequencing

Browser based quality control tool to expedite reviewing predicted variants in next generation sequencing files.

Simulator for structural variants in various types of next-generation sequencing data

Detection and Visualization of Exon-Level Copy Number Variants in Targeted Next Generation Sequencing Data

mitochondrial variant analysis tools

Filters for Next Generation Sequencing

Mouseexomesequencing ⭐ 6

A pipeline for variant calling from exome sequence data from murine tumors.

Rmahunter ⭐ 6

Pdxblacklist ⭐ 5

A database for genomic variation frequencies

A Bioconductor R-package for cell evaluation, characterisation and authentication using high throughput sequencing data.

Jseqarray.jl ⭐ 5

JSeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Julia

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