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. |