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Table 2 Short read sequence pre-processing algorithms in ngsShoRT

From: Software for pre-processing Illumina next-generation sequencing short read sequences

Category Algorithm/Method Description
Sequencing Artifacts Removal 5adpt Detects (using exact or approximate matching) sequencing artifacts listed in an input file and removes them.
rmHP Removes homopolymer sequences.
QSEQ Specific Methods qseq0 Removes QSEQ reads with “Failed_Chastity” filter flags.
qseqB Removes reads with more than certain number of "B"-scored bases.
Reads with “N” Bases Removal/Splitting nperc Filters out reads with un-called “N” bases exceeding a percentage cutoff.
ncutoff Filters out reads with un-called “N” bases exceeding a number cutoff.
nsplit Searches and removes “N” bases, then splits the read around the removed “N” bases into two smaller daughter reads.
Quality Score Based Trimming LQR Removes “low quality” reads using quality score cutoff or percent cutoff.
Mott Quality-window extraction (trim both the 5'- and 3'-ends of a read).
TERA Trims low quality-score bases from the 3'-ends of reads based on their running average quality scores.
5'/3'-end Bases Trimming 3end Trims bases from 3'-end of a read.
5end Trims bases from 5'-end of a read.