Table 1

Main features of various adapter trimmers
Adapter trimming Quality control Other
Method 5’ 3’ SE PE LMP Multi Ns Q Barcode Merge gzip Files MT
FastX × × × × × × × ×
SeqTrim × × × × ×
TagCleaner × × × × × × × × ×
EA-Tools × × × × ×
Cutadapt × × × × ×
TrimGalore × × × × × × ×
SeqPrep × × × × × × × × ×
Btrim × × × × × ×
Scythe × × × × × × × × ×
Flexbar × ×
Trimmomatic × × × × ×
AdapterRemoval × × × × ×
AlienTrimmer × × × × × ×
NextClip × × × × × × × × × × ×
Skewer ×

For each method, the table shows if it is able to: i) identify adapters in the 5’ end of reads, ii) identify adapters in the 3’ end of reads, iii) process single-end (SE) reads, iv) process paired-end (PE) reads, v) process Nextera long mate-pair (LMP) reads, vi) search for multiple different adapters (Multi), vii) trim subsequences of multiple degenerative characters (Ns), viii) trim low-quality nucleotides (Q), ix) separate multiplexed reads based on barcodes, x) merge overlapped pairs into longer single-end reads, xi) process gzip files directly, and xii) run with multiple threads simultaneously (MT). (○: Yes; ×: No).

Jiang et al.

Jiang et al. BMC Bioinformatics 2014 15:182   doi:10.1186/1471-2105-15-182

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