ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing

Matt Massie, Frank Nothaft, Christopher Hartl, Christos Kozanitis, André Schumacher, Anthony D. Joseph and David A. Patterson

EECS Department
University of California, Berkeley
Technical Report No. UCB/EECS-2013-207
December 15, 2013

http://www.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.pdf

Current genomics data formats and processing pipelines are not designed to scale well to large datasets. The current Sequence/Binary Alignment/Map (SAM/BAM) formats were intended for single node processing. There have been attempts to adapt BAM to distributed computing environments, but they see limited scalability past eight nodes. Additionally, due to the lack of an explicit data schema, there are well known incompatibilities between libraries that implement SAM/BAM/Variant Call Format (VCF) data access.

To address these problems, we introduce ADAM, a set of formats, APIs, and processing stage implementations for genomic data. ADAM is fully open source under the Apache 2 license, and is implemented on top of Avro and Parquet for data storage. Our reference pipeline is implemented on top of Spark, a high performance in-memory map-reduce system. This combination provides the following advantages:

1) Avro provides explicit data schema access in C/C++/C#, Java/Scala, Python, php, and Ruby; 2) Parquet allows access by database systems like Impala and Shark; and 3) Spark improves performance through in-memory caching and reducing disk I/O.

In addition to improving the format’s cross-platform portability, these changes lead to significant performance improvements. On a single node, we are able to speedup sort and duplicate marking by 2×. More importantly, on a 250 Gigabyte (GB) high (60×) coverage human genome, this system achieves a 50× speedup on a 100 node computing cluster (see Table 1), fulfilling the promise of scalability of ADAM.

The ADAM format provides explicit schemas for read and reference oriented (pileup) sequence data, variants, and genotypes. As the schemas are implemented in Apache Avro—a cross-platform/language serialization format—they eliminate the need for the development of language-specific libraries for format decoding/encoding, which eliminates the possibility of library incompatibilities.

A key feature of ADAM is that any application that implements the ADAM schema is compatible with ADAM. This is important, as it prevents applications from being locked into a specific tool or pattern. The ADAM stack is inspired by the “narrow waist” of the Internet Protocol (IP) suite (see Figure 2). We consider the explicit use of a schema in this format to be the greatest contribution of the ADAM stack.

In addition to the advantages outlined above, ADAM eliminates the file headers in modern genomics formats. All header information is available inside of each individual record. The variant and genotype formats also demonstrate two significant improvements. First, these formats are co-designed so that variant data can be seamlessly calculated from a given collection of sample genotypes. Secondly, these formats are designed to flexibly accommodate annotations without cluttering the core variant/genotype schema. In addition to the benefits described above, ADAM files are up to 25% smaller on disk than compressed BAM files without losing any information.

The ADAM processing pipeline uses Spark as a compute engine and Parquet for data access. Spark is an in-memory MapReduce framework which minimizes I/O accesses. We chose Parquet for data storage as it is an open-source columnar store that is designed for distribution across multiple computers with high compression. Additionally, Parquet sup- ports efficient methods (predicates and projections) for accessing only a specific segment or fields of a file, which can provide significant (2-10×) additional speedup for genomics data access patterns.


BibTeX citation:

@techreport{Massie:EECS-2013-207,
    Author = {Massie, Matt and Nothaft, Frank and Hartl, Christopher and Kozanitis, Christos and Schumacher, André and Joseph, Anthony D. and Patterson, David A.},
    Title = {ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2013},
    Month = {Dec},
    URL = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.html},
    Number = {UCB/EECS-2013-207},
    Abstract = {Current genomics data formats and processing pipelines are not designed to scale well to large datasets. The current Sequence/Binary Alignment/Map (SAM/BAM) formats were intended for single node processing. There have been attempts to adapt BAM to distributed computing environments, but they see limited scalability past eight nodes. Additionally, due to the lack of an explicit data schema, there are well known incompatibilities between libraries that implement SAM/BAM/Variant Call Format (VCF) data access.

To address these problems, we introduce ADAM, a set of formats, APIs, and processing stage implementations for genomic data. ADAM is fully open source under the Apache 2 license, and is implemented on top of Avro and Parquet for data storage. Our reference pipeline is implemented on top of Spark, a high performance in-memory map-reduce system. This combination provides the following advantages:

1) Avro provides explicit data schema access in C/C++/C#, Java/Scala, Python, php, and Ruby;
2) Parquet allows access by database systems like Impala and Shark; and
3) Spark improves performance through in-memory caching and reducing disk I/O.

In addition to improving the format’s cross-platform portability, these changes lead to significant performance improvements. On a single node, we are able to speedup sort and duplicate marking by 2×. More importantly, on a 250 Gigabyte (GB) high (60×) coverage human genome, this system achieves a 50× speedup on a 100 node computing cluster (see Table 1), fulfilling the promise of scalability of ADAM.

The ADAM format provides explicit schemas for read and reference oriented (pileup) sequence data, variants, and genotypes. As the schemas are implemented in Apache Avro—a cross-platform/language serialization format—they eliminate the need for the development of language-specific libraries for format decoding/encoding, which eliminates the possibility of library incompatibilities.

A key feature of ADAM is that any application that implements the ADAM schema is compatible with ADAM. This is important, as it prevents applications from being locked into a specific tool or pattern. The ADAM stack is inspired by the “narrow waist” of the Internet Protocol (IP) suite (see Figure 2). We consider the explicit use of a schema in this format to be the greatest contribution of the ADAM stack.

In addition to the advantages outlined above, ADAM eliminates the file headers in modern genomics formats. All header information is available inside of each individual record. The variant and genotype formats also demonstrate two significant improvements. First, these formats are co-designed so that variant data can be seamlessly calculated from a given collection of sample genotypes. Secondly, these formats are designed to flexibly accommodate annotations without cluttering the core variant/genotype schema. In addition to the benefits described above, ADAM files are up to 25% smaller on disk than compressed BAM files without losing any information.

The ADAM processing pipeline uses Spark as a compute engine and Parquet for data access. Spark is an in-memory MapReduce framework which minimizes I/O accesses. We chose Parquet for data storage as it is an open-source columnar store that is designed for distribution across multiple computers with high compression. Additionally, Parquet sup- ports efficient methods (predicates and projections) for accessing only a specific segment or fields of a file, which can provide significant (2-10×) additional speedup for genomics data access patterns.}
}

EndNote citation:

%0 Report
%A Massie, Matt
%A Nothaft, Frank
%A Hartl, Christopher
%A Kozanitis, Christos
%A Schumacher, André
%A Joseph, Anthony D.
%A Patterson, David A.
%T ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing
%I EECS Department, University of California, Berkeley
%D 2013
%8 December 15
%@ UCB/EECS-2013-207
%U http://www.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.html
%F Massie:EECS-2013-207