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cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.
Toshiki Takeuchi1, Atsuo Yamada1, Takashi Aoki1
1Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan.
Source Code for Biology and Medicine
|August 19, 2016
Summary
cljam is a new tool that processes next-generation sequencing data in Sequence Alignment/Map (SAM) and Binary Alignment (BAM) formats. It offers fast, parallel processing comparable to SAMtools but with simpler implementation.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Next-generation sequencing generates large datasets stored in Sequence Alignment/Map (SAM) and Binary Alignment (BAM) formats.
- SAMtools is a widely used tool for manipulating SAM/BAM files but requires additional libraries for parallel processing.
- Efficient parallelization tools are needed to handle the increasing volume of sequencing data in various computing environments.
Purpose of the Study:
- To develop a simplified parallel programming tool for handling SAM/BAM data.
- To create a solution that supports both cloud and PC cluster environments.
- To offer a high-performance alternative for processing next-generation sequencing data.
Main Methods:
- Developed cljam, a tool written in the Clojure programming language.
- Leveraged Clojure's capabilities for simplified parallel programming.
- Ensured compatibility with Java runtime environments across different operating systems (Windows, Linux, Mac OS X).
Main Results:
- cljam enables high-speed, parallel processing of SAM/BAM files.
- Execution times with cljam are comparable to those of SAMtools.
- The cljam codebase is concise, written in Clojure.
Conclusions:
- cljam provides an efficient and easy-to-implement solution for parallel processing of genomic data.
- The tool achieves performance on par with established tools like SAMtools.
- cljam's development in Clojure offers advantages in code simplicity and maintainability.
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