Sequencing and Raw Sequence Data Quality Control    ◾    45

adaptor trimming. This program is specifically fast and easy to use as part of a pipeline.

Moreover, it is able to identify adaptor sequences and trim them without the need of pro-

viding adaptor sequences [16].

1.7  SUMMARY

The NGS produces short reads that are widely used for the different sequencing applica-

tions for the high accuracy and low cost. However, the long reads produced by the TGS

(Pacific Bioscience and Oxford Nanopore Technologies) have also gained some popularity

in applications like de novo assembly, metagenomics, and epigenetics. The accuracy of the

long-read technologies has been substantially improved, but the cost is still high and less

affordable when they are compared to short-read technologies. The sequencing depth and

base call quality are the two crucial factors for most applications, and the analysts must

keep looking at them before proceeding with the analysis. Most HTS instruments per-

form quality control before delivering raw sequence data in FASTQ files. However, per base

qualities and other quality metrics must be assessed before using raw data in any analysis.

FIGURE 1.37  Trimmomatic processed reverse FASTQ file.