A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (make sure you fork from there)
☆21Sep 6, 2016Updated 9 years ago
Alternatives and similar repositories for piper
Users that are interested in piper are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Snakemake library for bioinformatics programs, with a focus on next-generation sequencing☆22Feb 4, 2016Updated 10 years ago
- The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline☆33Jan 20, 2018Updated 8 years ago
- Documenting usage and experience with bioinformatic tools☆40Sep 11, 2015Updated 10 years ago
- WES HLA Typing based on multiple alternative tools☆18Mar 8, 2021Updated 5 years ago
- Samwell: a python package for using genomic files... well☆20Jun 28, 2022Updated 3 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Structural variant pipeline☆18Jun 25, 2020Updated 5 years ago
- Survival analysis utility functions using functional programming principals☆11Jul 8, 2020Updated 5 years ago
- Parallel merging, squaring off and ensemble calling for genomic variants☆20Sep 17, 2019Updated 6 years ago
- SAMtools: A Primer☆13Dec 19, 2014Updated 11 years ago
- Efficient base quality score recalibrator for NGS data☆24Nov 28, 2015Updated 10 years ago
- A merged read deduplication tool capable to perform merged read deduplication on single end data.☆13Sep 4, 2024Updated last year
- SmallSeqFlow: A streamlined, notebook-based bulk RNA-seq analysis pipeline optimized for small-sample studies with modular extensions.☆18Feb 23, 2025Updated last year
- Bioinformatics Ketrew Pipelines☆28Nov 14, 2021Updated 4 years ago
- A new web-based HTML5 genome browser. Genome Maps can also browse BAM and VCFs files among other formats.☆27Sep 24, 2013Updated 12 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Source code for the program MavericK, described fully at www.bobverity.com/maverick☆12Jun 21, 2018Updated 7 years ago
- The integrated pipeline for Indel detection☆17Apr 29, 2018Updated 7 years ago
- Faster multispecies coalescent inference using multilocus data☆15Aug 13, 2023Updated 2 years ago
- CRUK Bioinformatics Workshop September 2017☆18Sep 21, 2017Updated 8 years ago
- ☆18Sep 28, 2015Updated 10 years ago
- Genome Annotation for the Masses☆36Jul 9, 2017Updated 8 years ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Feb 12, 2022Updated 4 years ago
- Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis☆18Nov 2, 2022Updated 3 years ago
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Parallel read alignment and variant calling using MapReduce☆18Feb 19, 2019Updated 7 years ago
- Variant calling from sequence reads using cloud computing☆40Jan 14, 2014Updated 12 years ago
- AncestralPaths is a local ancestry painting technique based on genealogies produced by RELATE. The method aims to assign 'path' ancestrie…☆11Jun 29, 2023Updated 2 years ago
- Code repository for the HAYSTAC pipeline☆15Oct 25, 2024Updated last year
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆32Apr 1, 2026Updated 2 weeks ago
- AdapterRemoval v2 - rapid adapter trimming, identification, and read merging☆116Updated this week
- JIP Pipeline System☆19Feb 5, 2018Updated 8 years ago
- ☆13Dec 3, 2024Updated last year
- ☆18Feb 11, 2026Updated 2 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Bryan talk at JSM 2015 re: are statisticians data scientists☆18Oct 30, 2015Updated 10 years ago
- A Perl extension and collection of utilities for Next-Generation Sequencing (NGS) data analysis☆23Oct 31, 2025Updated 5 months ago
- PharmGKB NGS Pipeline☆19Oct 2, 2018Updated 7 years ago
- Genotype likelihood simulator for VCF/BCF files☆16May 7, 2025Updated 11 months ago
- Tool to find regions of homozygosity (ROHs) from sequencing data.☆35Jun 17, 2024Updated last year
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆14May 1, 2023Updated 2 years ago
- Population Stratification Analysis on Genomics Data Using Deep Learning☆25Sep 5, 2016Updated 9 years ago