Software for pre-processing Illumina next-generation sequencing short read sequences

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].

ISSN: 1751-0473