CRG-CNAG / CalliNGS-NFView external linksLinks
GATK RNA-Seq Variant Calling in Nextflow
☆138Dec 14, 2022Updated 3 years ago
Alternatives and similar repositories for CalliNGS-NF
Users that are interested in CalliNGS-NF are comparing it to the libraries listed below
Sorting:
- Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices☆11Feb 20, 2020Updated 5 years ago
- A curated list of nextflow based pipelines☆621Jun 23, 2025Updated 7 months ago
- Nextflow implementation of the smoove workflow and other tools for SV calling and QC☆12Nov 12, 2020Updated 5 years ago
- Whole Genome Sequenceing Structural Variation Pipelines☆18Apr 4, 2019Updated 6 years ago
- Visualisation and prioritisation of genomic variants from human exome sequencing projects☆13Apr 23, 2019Updated 6 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Apr 7, 2022Updated 3 years ago
- Nextflow implementation of the GATK HaplotypeCaller pipeline☆13Dec 27, 2025Updated last month
- Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing☆133Jan 27, 2020Updated 6 years ago
- An automated RNA-seq pipeline using Nextflow☆37Dec 17, 2025Updated last month
- Allele frequency filtering for Mendelian variant discovery☆18Sep 27, 2016Updated 9 years ago
- ☆15Apr 2, 2025Updated 10 months ago
- Structural variant pipeline☆18Jun 25, 2020Updated 5 years ago
- Nextflow basic tutorial for newbie users☆33Jun 17, 2018Updated 7 years ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆546Updated this week
- Nextflow language support for Visual Studio Editor☆37Jan 23, 2026Updated 3 weeks ago
- Adapted from the GATK best practice guide to preprocess whole exome sequencing (WES) data☆11Sep 4, 2019Updated 6 years ago
- YAMP: Yet Another Metagenomic Pipeline☆62Jun 5, 2023Updated 2 years ago
- Genotype Imputation Pipeline for H3Africa☆24Nov 5, 2024Updated last year
- RNA-seq analysis pipeline for detection of gene-fusions☆170Updated this week
- See the main fork of this repository here >>>☆39Updated this week
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆58Feb 17, 2022Updated 3 years ago
- Assembly and intrahost / low-frequency variant calling for viral samples☆15Feb 12, 2020Updated 6 years ago
- Framework to benchmark algorithms when detecting germline copy number variations (CNVs) from NGS data☆14Dec 24, 2024Updated last year
- Example Nextflow pipelines and programming techniques☆107Sep 19, 2025Updated 4 months ago
- a tool for predicting mitochondrial DNA deletions using soft-clipping☆23Feb 3, 2022Updated 4 years ago
- Variant Calling Pipeline Using GATK4 and Nextflow☆59Feb 16, 2023Updated 3 years ago
- A curated collection of Nextflow implementation patterns☆368Nov 21, 2023Updated 2 years ago
- Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools☆84Sep 13, 2021Updated 4 years ago
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,201Updated this week
- Strelka2 germline and somatic small variant caller☆389Dec 29, 2021Updated 4 years ago
- Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores …☆16Aug 9, 2018Updated 7 years ago
- A tool set for short variant discovery in genetic sequence data.☆204May 4, 2021Updated 4 years ago
- GATK4 Best Practice Nextflow Pipeline☆33Jan 18, 2018Updated 8 years ago
- V'DJer - B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data☆29Aug 9, 2022Updated 3 years ago
- RNA mapping pipeline☆18Jun 3, 2018Updated 7 years ago
- Customer workshop materials☆19May 11, 2023Updated 2 years ago
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- Please consider using/contributing to https://github.com/nf-core/sarek☆18Jan 3, 2019Updated 7 years ago
- ☆14May 12, 2023Updated 2 years ago