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 |