Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
☆86Sep 13, 2021Updated 4 years ago
Alternatives and similar repositories for gatk4-rnaseq-germline-snps-indels
Users that are interested in gatk4-rnaseq-germline-snps-indels 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 processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools☆54Dec 19, 2019Updated 6 years ago
- STAR-Fusion codebase☆254Apr 18, 2026Updated 3 months ago
- Detect key Units in mosaic Tandem Repeats from representative reads from the same locus☆10Aug 2, 2023Updated 2 years ago
- Transposable element expression at unique loci in single cells with CELLO-seq☆12Jun 17, 2024Updated 2 years ago
- Tool for assessing/improving assembly quality in extra-long tandem repeats☆49Feb 23, 2021Updated 5 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Improved Phased Assembler☆29Mar 11, 2022Updated 4 years ago
- Reducing reference bias using multiple population reference genomes☆34May 27, 2024Updated 2 years ago
- VCF files of SVs using long-read sequencing (LRS).☆22Dec 17, 2021Updated 4 years ago
- ☆20Jan 6, 2024Updated 2 years ago
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆79Jan 13, 2026Updated 6 months ago
- Structural variant caller☆55Dec 8, 2021Updated 4 years ago
- Python package to interactively annotate histological images within a jupyter notebook☆18Oct 20, 2025Updated 9 months ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆124May 24, 2026Updated last month
- ☆17Jul 13, 2026Updated last week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆39Nov 27, 2024Updated last year
- tutorials for spateo package☆21Dec 25, 2024Updated last year
- Interpretable prioritization of splice variants in diagnostic next-generation sequencing☆18May 9, 2024Updated 2 years ago
- Visualisation and prioritisation of genomic variants from human exome sequencing projects☆13Apr 23, 2019Updated 7 years ago
- Readme☆10Mar 15, 2020Updated 6 years ago
- ☆14Feb 24, 2020Updated 6 years ago
- Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.☆11Jul 8, 2025Updated last year
- An analysis of Arabidopsis RNA-seq data (hy5 mutant and wt, two replicates each; SRA accession SRX029582)☆16Jul 3, 2012Updated 14 years ago
- ☆27Oct 22, 2025Updated 9 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- GATK RNA-Seq Variant Calling in Nextflow☆137Dec 14, 2022Updated 3 years ago
- Annotation and segmentation of MAS-seq data☆20May 25, 2023Updated 3 years ago
- Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. Please download the R package from the RaceID3…☆15Dec 7, 2018Updated 7 years ago
- Compute N50/NG50 and auN/auNG☆33Oct 7, 2023Updated 2 years ago
- GERP++ code from Sidow Lab modified by Kevin Thornton to compile properly.☆25Sep 19, 2016Updated 9 years ago
- GERMLINE is an algorithm for inferring long shared segments of Identity by Descent (IBD) between pairs of individuals in a large populati…☆16Apr 5, 2019Updated 7 years ago
- This tool designs guides for use with the base editor technology.☆13Aug 11, 2023Updated 2 years ago
- Scripts to reproduce the analysis of the MAESTER paper (https://www.nature.com/articles/s41587-022-01210-8).☆14May 18, 2024Updated 2 years ago
- The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, cl…☆15Feb 27, 2019Updated 7 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.
- SKATE R Utilities☆10Mar 7, 2026Updated 4 months ago
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆567Updated this week
- An R Package based on JavaScript libraries for Visualization of Interactive Circos Plot☆28Jul 26, 2022Updated 3 years ago
- Identification of segmental duplications in the genome☆29Mar 1, 2022Updated 4 years ago
- ☆17May 22, 2025Updated last year
- Interactive eQTL visualizations☆14Dec 12, 2022Updated 3 years ago
- Tools for working with BUS files☆102May 27, 2025Updated last year