With this option selected, the software inspects only the 3’ends of reads for consecutive low quality base calls. For Illumina and SOLiD System reads, the second half of the read is examined. NextGENe searches for the first base from the 3’end that has a quality value above the threshold. If no such bases are found, the entire read is removed. If the software finds a base that is above the threshold, it then searches the second half of the read from the 5’ end for at least “X” number of consecutive bases below the threshold. If this condition is met, the read is trimmed from this point back to the 3’ end of the read.

For Roche reads, only the last 20% of the read is examined. The software starts at the 5’ end of the last 20% of the read to find a base with a quality score above the threshold. When a base is found with a score above the threshold, the software then searches for at least “X” number of consecutive bases with scores below the threshold. When this condition is met, the read is trimmed from this point back to the 3’ end of the read. Homopolymers are ignored.