Table 1.

Comparison of ngsShoRT with other publically available pre-processing tools

Tool	Programming language	Targeted NGS platform	Input format	PE reads handling	Parallel processing	NGS artifacts handling	Quality score-based trimming	Output format	Summary report
ngsShoRT (2.1)	Perl	454, Illumina	FastQ, Illumina QSEQ	Yes	Yes	Yes	Yes: 3'-end, quality window and filter out low quality reads	FastQ	Yes
NGS QC toolkit (v.2.3.2) [15]	Perl	454, Illumina1	FastQ, FastA (+ .qual)	Yes	Yes	Yes	Yes: filter out low quality reads	FastA (+.qual), FastQ	Yes
FASTX toolkit (v. 0.0.13.2) [26]	C/C++	Non-specific	FastQ2, FastA (not .qual)	No	No	No	Yes: filter out low quality reads	FastA, FastQ	No
SeqTrim [25]	Perl	Non-specific3	FastA (+ .qual), Phred	No	No	No	Yes: filter out low quality reads	FastA (+.qual)	Yes
CutAdapt (v.1.3) [14]	Python4	454, Illumina, SOLID5	FastQ, SOLID’s cs.FastA + cs.FastA.qual	No	No	No	Yes: filter out low quality reads	FastQ, SOLID’s cs.FastA + cs.FastA.qual	No
Btrim [27]	C++6	Illumina	FastQ6	No	No	No	Yes: quality window	FastQ	No
SolexaQA (v.2.2) [8]	Perl	Illumina	FastQ	Yes	No	No7	Yes: quality window and filter out low quality reads	FastQ	Yes
Sickle [28]	C/C++8	Illumina	FastQ	Yes	No	No	Yes: quality window	FastQ	Yes
Scythe [24]	C/C++8	Illumina	FastQ	No	No	Yes, but only 3’	No	FastQ	Yes
Trimmomatic (v.0.32) [16]	Java	Illumina	FastQ	Yes	Yes	Yes	Yes: quality window and filter out low quality reads	FastQ	Yes

¹NGS QC’s IlluQC only works for FastQ file, and 454QC only works for FastA (+.qual) file [15].

²FASTX toolkit does not accept multi-line FastQ file and requires reformatting to one-line FastQ file using provided tools [26].

³While SeqTrim isn’t platform-specific, it can only take FastA file (with/without .qual and chromatogram) [25].

⁴Most of CutAdapt is in python, but the alignment algorithm was written in C for speedup [14].

⁵CutAdapt was designed with RNA-Seq technology in mind [14].

⁶Btrim’s C++ implementation is designed for single reads. The tool website offers an un-optimized Perl script that organizes separately trimmed paired-end files [27].

⁷SolexaQA does not provide primer/adapter trimming [8].

⁸Scythe and Sickle require Zlib (http://www.zlib.net/) [24,28].