A fast, scalable genome analysis system
Project description
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.
Documentation
ADAM’s documentation is hosted at readthedocs.
Python Requirements
ADAM depends on having PySpark installed.
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