Trimmomatic: A Flexible Trimmer for Illumina Sequence Data

Read pre-processing is an important first step to optimize the analysis
of next generation sequencing data by removing technical artifacts which
may interfere with downstream analysis. It is particularly important in
de-novo genome assembly projects, since technical sequences like
adapters can easily be incorporated as part of the target genome.

Trimmomatic is primarily targetted at data from Illumina sequencers, and
offers a range of sequence processing steps which can be flexibly
combined as need to suit user requirements.

Paired end data is not only supported, but actually helps ensure highly
accurate identification of the most common source of contamination:
'read-through' of short DNA fragments into the adapters. The tool also
tracks the paired state of processed data to produces separate paired
and unpaired files, ensuring that downstream tools which require paired
data can be used without problems.

Two main approaches to quality trimming are provided, a standard
'sliding window' approach, and a 'maximum information' approach which
balances the cost/benefits of additional, potentially erroneous data.

Additional processing steps for read cropping, filtering of entire reads
by length or quality are also included.

The tool was originally developed as an in-house tool for the S.
pennellii genome sequencing project, and proved both effective and
efficient on the large datasets needed for this project.