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Table 1 Comparison of ngsShoRT with other publically available pre-processing tools

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

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
  1. 1NGS QC’s IlluQC only works for FastQ file, and 454QC only works for FastA (+.qual) file [15].
  2. 2FASTX toolkit does not accept multi-line FastQ file and requires reformatting to one-line FastQ file using provided tools [26].
  3. 3While SeqTrim isn’t platform-specific, it can only take FastA file (with/without .qual and chromatogram) [25].
  4. 4Most of CutAdapt is in python, but the alignment algorithm was written in C for speedup [14].
  5. 5CutAdapt was designed with RNA-Seq technology in mind [14].
  6. 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].
  7. 7SolexaQA does not provide primer/adapter trimming [8].
  8. 8Scythe and Sickle require Zlib (http://www.zlib.net/) [24, 28].