Full GATK SNP calling pipeline
☆24Oct 30, 2025Updated 8 months ago
Alternatives and similar repositories for gatk-snp-calling
Users that are interested in gatk-snp-calling are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Code associated with the manuscript "A complete reference genome improves analysis of human genetic variation".☆17Jan 17, 2023Updated 3 years ago
- Gene Prediction using MAKER, CEGMA, SNAP, GENEMARK & AUGUSTUS☆10Jul 20, 2017Updated 9 years ago
- Various scripts that I have created that are useful for genome annotation (repeats & proteins)☆17Feb 21, 2022Updated 4 years ago
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 5 years ago
- Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as p…☆11Jun 25, 2019Updated 7 years 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.
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated 2 years ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 6 months ago
- Imputation-beagle-tutorial☆39Jun 2, 2022Updated 4 years ago
- Perform GWAS with gemma in a simple pipeline☆27Apr 26, 2025Updated last year
- MODAS: Multi-Omics Data Association Study toolkit☆21Nov 21, 2024Updated last year
- A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framewor…☆34Mar 18, 2014Updated 12 years ago
- Preprocessing sequencing data for allele-specific analysis☆13Mar 11, 2025Updated last year
- Plotly BioVisualization 🎯 Interactive Needle and Manhattan Plots & Alignment Viewer☆11Feb 28, 2020Updated 6 years ago
- ☆12Dec 1, 2020Updated 5 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- De novo lncRNA discovery pipeline, re-write of PLAR in shell and awk☆10Aug 2, 2023Updated 2 years ago
- A tool to visualize the haplotype pattern and various information in excel.☆24Mar 5, 2025Updated last year
- Set of script for the paper on the cattle graph genome☆14Jan 10, 2023Updated 3 years ago
- Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using…☆29Jul 8, 2026Updated last week
- A toolkit for identifying recombination and recombinant genotypes☆26Dec 3, 2025Updated 7 months ago
- Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣☆11Apr 28, 2023Updated 3 years ago
- ☆17Nov 26, 2023Updated 2 years ago
- Scripts for analysis used during the course☆98Apr 30, 2024Updated 2 years ago
- ☆12Jun 12, 2023Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- scripts for sequence and feature conversion, annotation, analysis ...☆28Mar 17, 2025Updated last year
- Accurate haplotype construction and detection of selection signatures enabled by 889 high quality pig genome sequences☆14May 11, 2023Updated 3 years ago
- ☆17Mar 7, 2025Updated last year
- A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes☆30Apr 10, 2024Updated 2 years ago
- ☆10Feb 25, 2024Updated 2 years ago
- 基因组组装注释流程及脚本☆16Feb 12, 2023Updated 3 years ago
- A Python package with integrated lncRNA prediction methods☆13Feb 17, 2021Updated 5 years ago
- ☆13Mar 22, 2022Updated 4 years ago
- In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Pra…☆16Oct 16, 2019Updated 6 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- A new simple and efficient software to PCA and Cluster For popolation VCF File☆83Jun 25, 2025Updated last year
- The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).☆21Sep 9, 2021Updated 4 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- Genome Annotation Pipeline☆45Aug 20, 2024Updated last year
- tips and tricks in genome-wide association studies - a tutorial☆14Jul 25, 2023Updated 2 years ago
- a Semi-automated pipeline for assembling T2T genome☆28Oct 16, 2025Updated 9 months ago
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆14Nov 20, 2023Updated 2 years ago