What does Timmomatic do?
From GcatWiki
Trimmomatic is a program that remove adapters from FastQ data so that this tagging information is not included in future data analysis and mapping.
Running FastQ data through trimmomatic increases quality control scores by removing lower quality reads form the data.
You can run trimmomatic on single reads or read pairs (Single end mode or Paired end mode). Paired mode uses data from paired reads to improve the likelihood of finding adapters and PCR primer fragments within the data by using forward and reverse reads of your data.
