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Table 1 Main features of various adapter trimmers

From: Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

 

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

×

  1. 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).