Trimming
Two types of trimming are available: quality trimming and adapter trimming.
Quality trimming
Raw reads are trimmed for low quality nucleotides. The quality limit used for trimming has been optimized for Illumina 150 bp paired end reads and cannot be adjusted.
It is possible to remove trimmed reads that are shorter than a defined threshold after quality trimming.
Adapter trimming
The algorithm can trim adapter sequences from mapped paired-end reads. For each individual read in a pair, read sequence that extends beyound the 5' end of the other read in the pair, is considered adapter sequence and is trimmed.
The consensus sequences for the removed R1 and R2 sequences, are included in the report.
It is possible to remove trimmed reads that are shorter than a defined threshold after adapter trimming.