johandahlberg / piper
A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (make sure you fork from there)
☆21Updated 8 years ago
Alternatives and similar repositories for piper:
Users that are interested in piper are comparing it to the libraries listed below
- Basic, no assumptions, multi-pileup☆24Updated 10 years ago
- variant integration methods for the 1000 Genomes Project☆21Updated 7 years ago
- reference free variant assembly☆33Updated last year
- Benchmarking toolkit for variant calling☆47Updated 4 years ago
- Toil workflows for common genomic pipelines☆33Updated 5 years ago
- Analysis Framework for Biological Data from High Throughput Experiments☆34Updated 8 years ago
- ☆14Updated 2 years ago
- robust matching of small variant datasets using flexible scoring schemes☆10Updated 4 years ago
- PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)☆14Updated 7 years ago
- Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis☆18Updated 2 years ago
- Easily run WDL workflows on GCP☆13Updated 3 years ago
- A python script used to annotate genomic intervals.☆18Updated 4 years ago
- Parallel merging, squaring off and ensemble calling for genomic variants☆20Updated 5 years ago
- Novel Adjacency Identification with Barcoded Reads☆13Updated 2 years ago
- Library for indexing VCF files for random access searches by rsID☆17Updated last year
- Manuscript describing ChronQC is now available online in Bioinformatics☆18Updated 5 years ago
- Import a CWL workflow specification to Nextflow script (experimental)☆27Updated 6 years ago
- A Feature Density Estimator for High-Throughput Sequence Tags☆23Updated 3 years ago
- Graphical assessment of structrial variants using 10x genomics data☆10Updated 8 years ago
- A library for manipulating bioinformatics sequencing formats in Apache Spark☆32Updated 2 weeks ago
- Docker images of bioinformatics software☆21Updated 7 years ago
- A small repo for storing the code for making the files and html for CCRs.☆22Updated 5 years ago
- Samwell: a python package for using genomic files... well☆20Updated 2 years ago
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Updated 7 years ago
- The OpEx (Optimised Exome) pipeline☆9Updated 6 years ago
- Method for detecting STR expansions from short-read sequencing data☆62Updated 3 years ago
- variant discovery and annotation using GATK and Ensembl☆17Updated 11 years ago
- Library for visualising genomic features in Python.☆15Updated 7 years ago
- Automatic Packaging and Distribution of Bioinformatics Pipelines☆26Updated 7 years ago
- Divine: Prioritizing Genes for Rare Mendelian Disease in Whole Exome Sequencing Data☆13Updated 5 years ago