A Variant Caller, Distributed. Apache 2 licensed.
☆71Mar 11, 2019Updated 6 years ago
Alternatives and similar repositories for avocado
Users that are interested in avocado are comparing it to the libraries listed below
Sorting:
- Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly☆85Jan 13, 2018Updated 8 years ago
- Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.☆41Feb 13, 2026Updated 2 weeks ago
- An RNA pipeline built on top of ADAM. Apache 2 licensed.☆19Jan 19, 2018Updated 8 years ago
- ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 li…☆1,047Feb 13, 2026Updated 2 weeks ago
- A Bayesian method for doing transcriptome assembly from RNA-seq data☆25Feb 2, 2015Updated 11 years ago
- run-length BWT tools for genomic sequences☆19May 19, 2022Updated 3 years ago
- A scalable genome browser. Apache 2 licensed.☆126Dec 2, 2022Updated 3 years ago
- Variant calling from sequence reads using cloud computing☆40Jan 14, 2014Updated 12 years ago
- MEM mapper prototype☆13Nov 28, 2020Updated 5 years ago
- Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data☆298Sep 6, 2025Updated 6 months ago
- Compare assembly graph file formats☆16Jul 23, 2015Updated 10 years ago
- scRNAseq integration with triplet neural networks☆41Feb 2, 2026Updated last month
- Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.☆41Mar 2, 2025Updated last year
- Gust is a set of GPU extensions for Breeze.☆32Apr 10, 2015Updated 10 years ago
- A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (m…☆21Sep 6, 2016Updated 9 years ago
- Documentation for the Google Genomics cookbook.☆141May 20, 2020Updated 5 years ago
- tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data☆17Jun 4, 2019Updated 6 years ago
- Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework☆72Dec 2, 2022Updated 3 years ago
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆31Jan 19, 2021Updated 5 years ago
- Efficient base quality score recalibrator for NGS data☆24Nov 28, 2015Updated 10 years ago
- BigWig and BAM utilities☆103Mar 26, 2024Updated last year
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Apr 25, 2023Updated 2 years ago
- de Bruijn Graph REAd mapping Tool☆14Jul 12, 2017Updated 8 years ago
- Ready-to-go Parquet-formatted public 'omics datasets☆30Nov 2, 2015Updated 10 years ago
- Artisanal 🤣 bioinformatics tools and pipelines in Scala☆20Jan 28, 2020Updated 6 years ago
- A genotype query interface.☆136Mar 29, 2021Updated 4 years ago
- Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data☆40Feb 19, 2026Updated 2 weeks ago
- ☆13Feb 18, 2026Updated 2 weeks ago
- notes and materials from dbug meetings☆10Sep 26, 2018Updated 7 years ago
- Web application for clinical pharmacogenomic interpretation☆10Mar 3, 2017Updated 9 years ago
- Annotation of cryptic transposon variants using Hidden Markov Models to detect conserved terminal features.☆10Jan 27, 2026Updated last month
- Utility functions to extend and optimize GenomicRanges functionality.☆10Mar 6, 2025Updated 11 months ago
- An accelerated framework for manipulating and interpreting high-throughput sequencing data☆26Jul 9, 2013Updated 12 years ago
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- resource for unix and SGE beginners☆24Feb 17, 2023Updated 3 years ago
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Oct 31, 2019Updated 6 years ago
- Benchmarking toolkit for variant calling☆48Oct 13, 2020Updated 5 years ago
- Prescriptive Applications over Kite and Hadoop☆12Oct 14, 2015Updated 10 years ago
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 5 years ago