Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
☆574Jun 8, 2026Updated this week
Alternatives and similar repositories for sarek
Users that are interested in sarek are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- RNA-seq analysis pipeline for detection of gene-fusions☆174Jun 2, 2026Updated last week
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,311May 12, 2026Updated last month
- Call and score variants from WGS/WES of rare disease patients.☆117Updated this week
- Nanopore demultiplexing, QC and alignment pipeline☆227Apr 30, 2026Updated last month
- Pipeline to fetch metadata and raw FastQ files from public databases☆194May 29, 2026Updated 2 weeks 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.
- Test data to be used for automated testing with the nf-core pipelines☆163Jun 4, 2026Updated last week
- Personal Cancer Genome Reporter (PCGR)☆279Updated this week
- Nextflow training material☆249Updated this week
- Precision HLA typing from next-generation sequencing data☆80Jun 4, 2026Updated last week
- Converts bam or cram files to fastq format and does quality control.☆32Updated this week
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆858May 2, 2026Updated last month
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆557Jun 1, 2026Updated last week
- Repository to host tool-specific module files for the Nextflow DSL2 community!☆417Updated this week
- Plot structural variant signals from many BAMs and CRAMs☆567Jul 13, 2024Updated last year
- 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.
- ASCAT R package☆203Feb 12, 2026Updated 4 months ago
- A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …☆90Updated this week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,459May 20, 2026Updated 3 weeks ago
- B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework☆79Jun 5, 2026Updated last week
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆241May 27, 2026Updated 2 weeks ago
- TIDDIT - structural variant calling☆79Mar 22, 2026Updated 2 months ago
- Official code repository for GATK versions 4 and up☆1,965Updated this week
- A DSL for data-driven computational pipelines☆3,415Updated this week
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆330Updated this week
- 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.
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆59Apr 27, 2026Updated last month
- Python package with helper tools for the nf-core community.☆311Updated this week
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆192Jun 3, 2026Updated last week
- genetic variant expressions, annotation, and filtering for great good.☆275May 12, 2026Updated last month
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆335May 27, 2025Updated last year
- ATAC-seq peak-calling and QC analysis pipeline☆226May 26, 2026Updated 2 weeks ago
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆94Updated this week
- using all the bits for echt rapid variant annotation and filtering☆162Apr 30, 2026Updated last month
- Annotation and Ranking of Structural Variation☆300Updated 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.
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆320Apr 24, 2026Updated last month
- GATK RNA-Seq Variant Calling in Nextflow☆137Dec 14, 2022Updated 3 years ago
- Nextflow pipeline to convert VCF files into MAF files.☆10Dec 12, 2025Updated 6 months ago
- Simple test framework for Nextflow pipelines☆187Apr 27, 2026Updated last month
- (WIP) best-practices workflow for rare disease☆64Jul 1, 2024Updated last year
- Strelka2 germline and somatic small variant caller☆394Apr 20, 2026Updated last month
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆417May 25, 2026Updated 2 weeks ago