Filter based on Ns

Description

Filters out reads form a reads file based the number or percentage of unassigned nucleotides in a read.

Details

This tool utilizes the PRINSEQ package.
The filtering is calculated with PRIONSEQ 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 reads 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 write out the duplicate reads that are filtered out. These reads are stored to 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.

    Reference

    This tool is based on the PRINSEQ package.