Variant Calling Pipeline Using GATK4 and Nextflow
☆60Oct 8, 2026Updated last month
Alternatives and similar repositories for variant-calling-pipeline-gatk4
Users that are interested in variant-calling-pipeline-gatk4 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- GATK RNA-Seq Variant Calling in Nextflow☆137Dec 14, 2022Updated 3 years ago
- GAPPadder is tool for closing gaps on draft genomes with short sequencing data☆29Jun 1, 2017Updated 9 years ago
- TIDDIT - structural variant calling☆81Jul 20, 2026Updated 3 months ago
- Primer3Plus is an advanced web interface for primer3.☆46Apr 26, 2025Updated last year
- Assembly and intrahost / low-frequency variant calling for viral samples☆15Feb 12, 2020Updated 6 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Part1: fastq and bam processing and quality check. Part2: variant calling, filtering and annotation☆12Feb 2, 2024Updated 2 years ago
- A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framewor…☆33Mar 18, 2014Updated 12 years ago
- Advanced steps of the OSCA book☆17Aug 26, 2026Updated 2 months ago
- ☆15Aug 1, 2021Updated 5 years ago
- dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCF…☆11Feb 3, 2021Updated 5 years ago
- Snakemake workflow for neoantigen prediction☆15Sep 7, 2023Updated 3 years ago
- Workflows for germline short variant discovery with GATK4☆145May 7, 2021Updated 5 years ago
- An R package for annotation of circular RNAs☆11Mar 30, 2020Updated 6 years ago
- Using de-novo assembly and read-phasing to assemble reference-free diploid genomes☆23Mar 26, 2026Updated 7 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Alignment and variant-calling pipeline for Illumina HIV sequences.☆11May 19, 2020Updated 6 years ago
- Synteny Mapping and Analysis Program☆30Updated this week
- TRUST4 manuscript evaluation☆17Jul 8, 2022Updated 4 years ago
- This repository contains Jupyter Notebooks containing GATK Best Practices Workflows☆26Dec 19, 2019Updated 6 years ago
- convert a blast output to a bed file☆12Jun 19, 2015Updated 11 years ago
- MUM&Co uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation☆76Jan 12, 2026Updated 10 months ago
- ☆11Aug 20, 2019Updated 7 years ago
- Locate transgenic insertion sites☆11Mar 14, 2023Updated 3 years ago
- A structural variation pipeline for short-read sequencing☆211Updated this week
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/☆49Aug 20, 2025Updated last year
- Westlake BioBank for Chinese pilot project☆10May 17, 2023Updated 3 years ago
- Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.☆11Aug 11, 2026Updated 3 months ago
- SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package☆17Apr 17, 2020Updated 6 years ago
- Analysis scripts and notebooks for Numbat paper☆10Aug 12, 2022Updated 4 years ago
- This repository aims to serve as an index of the work described at Salmen & De Jonghe et. al 2022☆25Feb 21, 2022Updated 4 years ago
- Scripts for analyzing data displayed and deposited on the long non-coding RNA knowledgebase (lncRNAKB)☆11May 5, 2021Updated 5 years ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆621Updated this week
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Whole genome workflows☆13Nov 9, 2024Updated 2 years ago
- Small utility script to submit genomes to PHASTER for phage detection☆26Oct 21, 2021Updated 5 years ago
- Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the …☆28Jan 4, 2021Updated 5 years ago
- Annotation pipeline for plant genomes by PGSB☆11Nov 12, 2021Updated 5 years ago
- R package to estimate kinship and FST from SNP data☆21Jan 27, 2026Updated 9 months ago
- Circular RNA Identification for Nanopore Sequencing☆23May 23, 2024Updated 2 years ago
- Package to design primers for MutaSeq and related methods☆11Jan 15, 2021Updated 5 years ago
Are these results useful?