## Filtering / Filter reads for adapters, length and Ns

### Description

Given a FASTQ file, this tool filters reads based on whether they contain the given adapter sequence.

### Parameters

- Adapter sequence that is used for filtering and that is subsequently removed (...) [CCTTAAGG]
- Discard sequences shorter than (1-100) [15]

### Details

Adapters are clipped from the 3' end. If the read is too short after clipping, it is discarded. Also reads which contain unknown nucleotides (Ns) are discarded.

### Output

A FASTQ file containing reads which contained the adapter sequence, which are long enough, and which don't contain Ns. In addition a log file is produced, telling how many reads the input file contained and what percentage of them were discarded.

### Reference

This tool is based on the FASTA/Q Clipper tool of the FASTX package.