Accessible, useful an powerful Java library that makes use of the Hadoop MapReduce framework to manipulate bioinformatics files #Bioinformatics file manipulation #Adoop MapReduce framework #Java library #Genetics #Sequencer #Manipulation
Hadoop-BAM was created as an open source, Java-based library for distributed processing of genetic data from next generation sequencer machines.
It allows scalable manipulation of aligned reads in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM (Binary Alignment/Map) files that are processed using Hadoop.
Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions in the Hadoop map-reduce framework.
The library builds on top of the popular Picard SAM-JDK, so tools that rely on the Picard API are expected to be easily convertible to support large scale distributed processing.
System requirements
What's new in Hadoop-BAM 7.0:
- Switching from Picard/Samtools to HTSJDK
- First release to OSS Sonatype
- Renaming of packages
- Changes to VariantContextCodec: encoding of genotypes generated by other means than VCF import (thanks to Joel Thibault)
Hadoop-BAM 7.0
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