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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
PubMed
Summary
This summary is machine-generated.

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.

Keywords:
BAMClojureDNANext-generation sequencingParallel processingSAM

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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.