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QC plots and stats

The first step in the data preprocessing is to check the quality of bases in all the reads. Once we understand the quality spectrum of the reads, we can decide on the parameters for trimming low quality bases. If the raw reads are not demultiplexed, demultiplexing should be performed before proceeding to the next step. Illumina’s CASAVA or QIIME tools can perform the demultiplexing task.

Software: FASTQC, MutliQC, PRINSEQ, SolexaQA