Genome Analysis with MapReduce

Genome sequencing technology has been improved intensely, but the number of bases generated by modern sequencing techniques has also been growing at an exponential rate. There are next generation sequencing technologies working with large data sets of genome data, such as the 1000 Genomes Project. In the report we discuss analysis tools for next generation dna sequencing data using a structured programming framework called the Genome Analysis Toolkit (gatk). This framework is used to build genome analysis tools easily and efficiently by using the functional programming paradigm called MapReduce. MapReduce is a distributed programming framework which is used for processing and extracting knowledge from large data sets. The report also describes Hadoop, which is a software scheme for cloud computing that provides MapReduce functionality for computing clusters and Hadoop Distributed File System for storing large data. The report illustrates the use of MapReduce in Hadoop by running the simple WordCount class and an application called Hadoop-bam. As a part o