{"repo":"bigdatagenomics/adam","free":true,"listed":false,"github":"https://github.com/bigdatagenomics/adam","clone":"git clone https://github.com/bigdatagenomics/adam.git","description":"ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.","language":"Scala","stars":1057,"topics":["spark","big-data","bioinformatics","genomics","parquet","avro","scala","java","python","r"],"license":"Apache-2.0","category":"cli-tools","readme_excerpt":"ADAM ==== Introduction ADAM is a library and command line tool that enables the use of Apache Spark to parallelize genomic data analysis across cluster/cloud computing environments. ADAM uses a set of schemas to describe genomic sequences, reads, variants/genotypes, and features, and can be used with data in legacy genomic file formats such as SAM/BAM/CRAM, BED/GFF3/GTF, and VCF, as well as data stored in the columnar Apache Parquet format. On a single node, ADAM provides competitive performance to optimized multi-threaded tools, while enabling scale out to clusters with more than a thousand cores. ADAM's APIs can be used from Scala, Java, Python, R, and SQL. Why ADAM? Over the last decade, DNA and RNA sequencing has evolved from an expensive, labor intensive method to a cheap commodity. The consequence of this is generation of massive amounts of genomic and transcriptomic data . Typically, tools to process and interpret these data are developed with a focus on excellence of the results generated, not on scalability and interoperability . A typical sequencing workflow consists of a suite of tools from quality control, mapping, mapped read preprocessing, to variant calling or quantification, depending on the application at hand. Concretely, this usually means that such a workflow is implemented as tools glued together by scripts or workflow descriptions, with data written to files at each step. This approach entails three main bottlenecks: 1. scaling the workflow comes down to","default_branch":null,"files":null,"tree":[],"storefront":"/r/bigdatagenomics","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/bigdatagenomics/adam/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}