Filtering / Filter reads for adapters, length and Ns


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



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 optionally discarded.


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.


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