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Ios Twitter Image Pipeline ⭐ 1,838

Twitter Image Pipeline is a robust and performant image loading and caching framework for iOS clients

Awesome Nextflow ⭐ 448

A curated list of nextflow based pipelines

Copy number variant detection from targeted DNA sequencing

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

PEPPER-Margin-DeepVariant

Dna Seq Gatk Variant Calling ⭐ 138

This Snakemake pipeline implements the GATK best-practices workflow

Gwas_scripts ⭐ 127

Codebook from my GWAS cookbook

Gcp Variant Transforms ⭐ 114

GCP Variant Transforms

Fermikit ⭐ 91

De novo assembly based variant calling pipeline for Illumina short reads

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

Sentieon Scripts ⭐ 53

Helper scripts for biological data processing from Sentieon

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Mtoolbox ⭐ 44

A bioinformatics pipeline to analyze mtDNA from NGS data

Needlestack ⭐ 39

Multi-sample somatic variant caller

Mutation Identification Pipeline. Read the latest documentation:

List of IARC bioinformatics nextflow pipelines

Mtbseq_source ⭐ 32

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Gotcloud ⭐ 29

Genomes on the Cloud, Mapping & Variant Calling Pipelines

Persvade ⭐ 27

perSVade: personalized Structural Variation detection

Deepvariant ⭐ 26

Deep Variant as a Nextflow pipeline

Variant_calling_pipeline ⭐ 25

A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framework in Python.

Gbs Snp Crop ⭐ 24

GBS SNP Calling Reference Optional Pipeline

Sars Cov 2 ⭐ 23

SARS-CoV-2 variant calling and consensus assembly pipeline

Variant annotation and merging pipeline

Pipeline Umi Amplicon ⭐ 21

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

Use an ensemble of variant callers to call variants from ATAC-seq data

Maliampi ⭐ 19

Maximum Likelihood Amplicon Pipeline

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies

variant discovery and annotation using GATK and Ensembl

Topmed_variant_calling ⭐ 18

Sv Adjudicator ⭐ 17

Haplotypo ⭐ 17

This is the Haplotypo repository

Network_snps ⭐ 17

A framework for network analysis and display of SNPs

Gatk4 Genome Processing Pipeline ⭐ 16

Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

Roslin Variant ⭐ 15

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

Research pipeline for exploring clinically relevant genomic variants

Parallel read alignment and variant calling using MapReduce

Clinicalgradednaseq ⭐ 15

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

Umccrise ⭐ 14

🐍 DRAGEN Tumor/Normal workflow post-processing

Pipeline5 ⭐ 14

Variants2neoantigen ⭐ 14

a neoantigen calling pipeline begins from variants record file (MAF)

Annotatevariants ⭐ 14

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

Falcon Genome ⭐ 13

Falcon Accelerated Genomics Pipelines

Gatk Pipeline ⭐ 12

A shell script which implements GATK pipeline for variant calling.

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Variant Calling Pipeline ⭐ 11

HPC based pipelines for variant calling using GATK

De-novo Assembly Structural Variant Caller

Adult_brain_somatic_mosaicism ⭐ 11

This repository collects pipelines, codes, and some intermediate results for adult brain somatic mosaicism study.

Deepvariant On Spark ⭐ 11

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

Please consider using/contributing to https://github.com/nf-core/sarek

Assembly and intrahost / low-frequency variant calling for viral samples

Clin.iobio ⭐ 9

Clin.iobio - Workflow and reporting for iobio variant analysis pipeline

Structural variant pipeline

GATK pipeline compatible with Cirrus

Pdx_exomeseq ⭐ 9

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

An efficient genetic data imputation pipeline

Gatk For Microbes ⭐ 8

Gentb Site ⭐ 8

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens

Gatk4 Mitochondria Pipeline ⭐ 8

Workflow for SNP and INDEL variant calling on mitochondria.

Wgs Structvar ⭐ 8

Whole Genome Sequenceing Structural Variation Pipelines

Mb Gatk Sge ⭐ 8

SGE scripts / pipeline for running GATK/VEP on a cluster

Somaticwrapper ⭐ 8

Detect somatic variants from tumor and normal WGS/WXS data

Bigquery Genomics Qc ⭐ 7

Genomics QC pipeline

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

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Sentieon Dnascope Ml ⭐ 7

Sentieon DNAscope + Machine Learning Model

Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape

Machine learning framework to quantify pathogenicity of structural variants

Structural Variantcalling ⭐ 7

A workflow for calling structural variants. Category:Single-Sample

Run multiple Pipeline5 instances at once

Vargenius ⭐ 7

VarGenius is a software for variants discovery and annotation. It allows efficient management of folder data and jobs submission into a PBS cluster. All the variants will be inserted into a PostgreSQL database that can be used for downstream analyses. It is written with PERL, R and HTML languages and uses Picard, Samtools, BWA, GATK and Annovar!

Exomepipe ⭐ 7

WGS and Exome analysis pipeline

Kipoi Gwas ⭐ 6

Sperm_control_cohort_mosaicism ⭐ 6

This repository collects pipelines, codes, and some intermediate results for the study of mosaic SNV/Indels for sperm, blood, and other samples of a control cohort.

NGS workflow automation and related tools

Mouseexomesequencing ⭐ 6

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

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results

Hugodims Pipeline ⭐ 6

Source code of the pipeline for the Hugodims project.

Eva Pipeline ⭐ 5

Genomic variation pipeline for the European Variation Archive, implemented using Spring Batch

Indel_correction_pipeline ⭐ 5

new falcon assemblies that have been quivered and Pilon polished still have heterozygote indel errors. This pipeline will correct most of them.

For modeling genetic variation based on protein domains

Genetics Pipe ⭐ 5

Viral_variant_caller ⭐ 5

A nextflow pipeline to call single nucleotide and structural variants in viral populations

Pdxblacklist ⭐ 5

Android_tools ⭐ 5

A collection of tools I use for my Android CI/CD pipeline

Pipelines ⭐ 5

Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data

Bionode Example Dat Gasket ⭐ 5

Bionode Example with Dat and Gasket

Sqtlseeker2 Nf ⭐ 5

An automated sQTL mapping pipeline using Nextflow

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