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 This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.
☆28Jan 4, 2021Updated 5 years ago
Alternatives and similar repositories for gatk4-genome-processing-pipeline
Users that are interested in gatk4-genome-processing-pipeline are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Workflows for converting between sequence data formats☆40Sep 5, 2021Updated 5 years ago
- VCF file compressor reaching over 30-fold efficiency on massive genotype datasets, with processing speeds up to 100 MB/s and peak memory …☆19Oct 5, 2026Updated last month
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆56Oct 29, 2020Updated 6 years ago
- Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools☆162Aug 10, 2022Updated 4 years ago
- Workflows for germline short variant discovery with GATK4☆145May 7, 2021Updated 5 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆82Nov 30, 2018Updated 7 years ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆59Mar 19, 2020Updated 6 years ago
- ☆12Dec 4, 2023Updated 2 years ago
- A tool for diagnosing SMA in exome, genome or targeted sequencing data☆14Jul 1, 2026Updated 4 months ago
- A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample☆26Jul 27, 2026Updated 3 months ago
- Web-site for the 2020 CRUK CC Bioinformatics Summer School (Held virtually)☆25Mar 4, 2021Updated 5 years ago
- MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combin…☆12Jul 19, 2016Updated 10 years ago
- A structural variation pipeline for short-read sequencing☆210Updated this week
- ☆24Feb 22, 2023Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- CLI to automate Nextflow pipeline testing☆13Dec 15, 2025Updated 10 months ago
- A single-cell and spatial RNA-seq database for Alzheimer’s Disease☆28Jul 17, 2024Updated 2 years ago
- A nextflow pipeline for calling CNVs in probe-enriched sequencing workflows☆14Oct 20, 2026Updated 2 weeks ago
- code repository for Hutchins et al. "Reconstructing signaling history of single cells via statistical inference" (2025)☆13Sep 19, 2026Updated last month
- ☆10May 31, 2022Updated 4 years ago
- ☆12Aug 23, 2018Updated 8 years ago
- SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data☆20Jan 24, 2022Updated 4 years ago
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated last year
- Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)☆15Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.☆14Nov 11, 2019Updated 6 years ago
- PgRC: Pseudogenome based Read Compressor☆14Nov 20, 2024Updated last year
- In-silico doublet annotation for single cell RNA sequencing data☆11Jan 7, 2026Updated 10 months ago
- Best-practice analysis pipeline for mapping reads to a (large) collections of genomes☆13Oct 26, 2026Updated last week
- ☆10Mar 5, 2019Updated 7 years ago
- Tests Allelic Expression data for extreme imbalance w.r.t. population☆11Oct 8, 2021Updated 5 years ago
- ☆10Jul 19, 2024Updated 2 years ago
- Supporting information of 'Single-cell RNA sequencing of a European and an African lymphoblastoid cell line'☆11Feb 27, 2020Updated 6 years ago
- Repository containing the code to reproduce the analyses contained in the MEFISTO manuscript☆13Jul 27, 2021Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Fast HLA type inference from whole-genome data☆149Apr 3, 2025Updated last year
- Method to detect exonic CNVs in NGS Gene Targeted Panels☆16Dec 3, 2019Updated 6 years ago
- Determining tandem repeat lengths using raw nanopore signals.☆15Sep 11, 2023Updated 3 years ago
- WDL tools for parsing, type-checking, and more☆28May 2, 2026Updated 6 months ago
- ☆12Sep 4, 2022Updated 4 years ago
- Analyze exome data for Mendelian disorders. Still in alpha-testing.☆10Apr 13, 2016Updated 10 years ago
- Nextflow training material for introductory tutorial☆109May 13, 2022Updated 4 years ago