The next generation sequencing(NGS) technology is playing an increasingly prominent role in capturing DNA and RNA sequencing by producing high-throughput sequences (HTS). The major challenge with HTS is the complexity and difficulty of data quality control (QC). Only a high quality data is capable for accurate diagnosis of the disease. For accurate diagnosis the data that needs to be analysed must be appropriate and correct. To fulfill this requirement, computer scientists have implemented the algorithms in easy to use manner that become convenient tools for biological research. The raw sequence generated by the NGS technologies is first cleaned and then moved further for clinical analysis. The step of cleaning includes removal of short sequences and trimming of inappropriate headers. This paper compares some popular, open source tools used for cleaning the captured sequences.

Illumina, FASTQ, FASTA, tag removal, single end, paired end

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