Read Preprocessing

Given that the data consists of short reads from Illumina, the sequences contain adapters and therefore need to be preprocessed in order to improve the read quality. This has to be done since, adapters and low quality base calls must be removed to increase the quality of the reads. Most of the reads provided for the purpose of this replication project have been preprocessed.

The software used for this purpose is Trimmomatic. The reads to be trimmed consisted of 2 forward & reverse reads, 1 forwards paired, 1 forwards unpaired, one reverse paired, and one reversed unpaired read.