Filter reads for Ns


Filters reads based the number or percentage of unassigned nucleotides (Ns).


This tool utilizes the PRINSEQ package.
The filtering is calculated with PRINSEQ options -ns_max_n and -ns_max_p.

  • If you define the "Maximum count of Ns" value, the reads that contain more the defined amount of Ns are filtered out.
  • If you define the "Maximum Percentage of Ns" value, the reads that contain higher percentage of Ns are filtered out.
  • Output

    The reads that pass the filtering condition are saved to file called accepted.fastq or accepted.fasta. You can also choose to store the reads that are filtered out to a separate file (rejected.fastq or rejected.fasta). You can also print out a log file that contains information about the filtering task and statistics about how many reads were accepted and rejected.


    This tool is based on the PRINSEQ package.