timpalpant / java-genomics-ioLinks
A simple and performant API for working with many genomic file formats in a consistent fashion
☆16Updated 7 years ago
Alternatives and similar repositories for java-genomics-io
Users that are interested in java-genomics-io are comparing it to the libraries listed below
Sorting:
- vcf file manipulation☆22Updated 10 years ago
- Flexible genotype query among 30,000+ samples whole-genome☆95Updated 5 years ago
- Workflow Description Language compiler for the DNAnexus platform☆41Updated 2 years ago
- The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data☆30Updated 7 years ago
- The Ensembl Variation Perl API and SQL schema☆29Updated 2 weeks ago
- Generate and process BAM files from Illumina sequencing instrument files☆23Updated 9 years ago
- (WIP) best-practices workflow for rare disease☆60Updated last year
- sort genomic data☆36Updated 5 years ago
- create a gemini-compatible database from a VCF☆56Updated 4 years ago
- VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications☆86Updated 10 months ago
- gvcf aggregation tool☆12Updated 7 years ago
- Utilities to create and analyze gVCF files☆38Updated 8 years ago
- Galaxy Github repository BETA 1. May be destroyed and recreated if post-conversion problems are found (but post-conversion commits on thi…☆12Updated 10 years ago
- Visualization and annotation of CNVs from population-scale whole-genome sequencing data☆72Updated 7 years ago
- Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang☆47Updated 5 years ago
- a pileup library that embraces the huge☆43Updated 4 years ago
- Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach☆36Updated 14 years ago
- Genome-wide reconstruction of complex structural variants☆39Updated 3 years ago
- Simple vcf parser, based on PyVCF☆46Updated 6 years ago
- Bring Your Own Bioinformatics☆27Updated 9 years ago
- FermiKit small variant calls for public SGDP samples☆17Updated 8 years ago
- ☆82Updated 6 years ago
- Tools for querying and analysis of genomic data☆27Updated last week
- Super small biological datasets for unit testing☆61Updated 5 years ago
- small RNA analysis from NGS data☆37Updated 11 months ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆56Updated 5 years ago
- Approach to identify simple and complex structural genomic rearrangements using a randomized approach☆21Updated 6 years ago
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Updated 5 years ago
- Ensembl tools☆35Updated 3 months ago
- An awk-like VCF parser☆56Updated last year