I am trying to use MATLAB for pre-processing of NGS data. Can anyone suggest a comprehensive code for this procedure. I have tried codes suggested in this page but the codes can only be used for a limited number of tasks. For example I don't know how to filter (or mask) reads shorter than 10 nucleotides or how to treat paired-end reads. Moreover, how can I filter reads that have more than two N nucleotides? can anyone suggest a comprehensive reference for these tasks?
MATLAB: How to pre-process Next Generation Sequencing data using MATLAB
Bioinformatics Toolboxhigh-throughput sequencing
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