NGS data processing with Hadoop
We are beginners, bachelor students and we should code Java-standalone application running on the Apache Hadoop system. We should implement a map/reduce approach and a non-map/reduce approach using Hadoop.
We should load FASTQ file, one read at a time and code some functions enabling queries on the data, for example, read length, count a fraction of bases, quality information,....
Can you suggest useful documentation or some code examples? Can you give us recommendations on how to begin, what to take in account?
Thank you in advance, We are very grateful for all the replies and tips.
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Maybe start by taking a look at a tool called FastQC, which is a Java software for fastq files QC.
We have done it already. All plots from FASTQC were generated. Now we are thinking of how to integrate it with Hadoop -.- Thank you for the suggestion.