Table 2 Characteristics of several popular tools for preprocessing NGS reads
From: From next-generation resequencing reads to a high-quality variant data set
Software | Ability of the software to: | Reference | ||
|---|---|---|---|---|
Handle multiple adapter sequences | Trim low-quality bases | Demultiplex barcodes | ||
AdapterRemoval | − | + | − | |
AlienTrimmer | + | + | − | |
Btrim | − | + | + | |
CONDETRI | − | + | − | |
Cutadapt | + | + | − | NA |
EA-Utils | − | + | + | NA |
ERNE-FILTER | − | + | − | |
FASTX-Toolkit | − | − | + | NA |
Flexbar | + | + | + | |
Kraken | + | + | + | |
NGSQC | + | + | − | |
ngsShoRT | + | + | − | |
PEAT | + | − | − | |
PRINSEQ | − | + | − | |
QC-Chain | + | + | − | |
QcReads | + | + | − | |
Reaper | + | + | + | NA |
SeqTrim | + | + | − | |
Sickle | − | + | − | NA |
Skewer | + | + | + | |
TrimGalore! | − | + | − | NA |
Trimmomatic | + | + | − | |
