ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Pilon is an automated genome assembly improvement and variant detection tool

Tools for working with genomic and high throughput sequencing data.

A scalable genome browser. Apache 2 licensed.

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

FlashFry: The rapid CRISPR target site characterization tool

A Variant Caller, Distributed. Apache 2 licensed.

Quality of RNA-Seq Toolset

Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.

Build and maintain multiple custom conda environments all in one place.

Tools to gather evidence for structural variation via breakpoint detection.

Artisanal 🤣 bioinformatics tools and pipelines in Scala

secondary analysis pipelines parallelized with apache spark

This repository is home to CALITAS, a CRISPR-Cas-aware ALigner for In silico off-TArget Search. CALITAS implements a customized gapped alignment of guide sequences to genomes and other reference se…

Collection of assorted tools for processing, filtering, annotating, organizing, merging, comparing, and reformatting variant data.