| Cutadapt |
1.1 |
code.google.com/p/cutadapt/downloads/list |
Python and C |
Running sum |
yes |
no |
no |
no |
Can also remove adapters, multi-threaded |
| ConDeTri |
2.2 |
code.google.com/p/condetri/ |
Perl |
Window based |
yes (since v2.2) |
yes |
no |
no |
|
| ERNE-FILTER |
1.2 |
sourceforge.net/projects/erne/files/ |
C++ |
Running sum |
yes |
yes |
yes |
yes |
Can be combined with contaminant removal, multi-threaded |
| FASTX quality trimmer |
0.0.13.2 |
hannonlab.cshl.edu/fastx_toolkit/download.html |
C++ |
Window based |
no |
no |
no |
no |
The default minimum read length parameter (-p) is set to zero |
| PRINSEQ |
0:19:05 |
sourceforge.net/projects/prinseq/files/ |
Perl |
Window based |
no |
no |
no |
yes |
Also web interface for medium-size data |
| Trimmomatic |
0.22 |
www.usadellab.org/cms/index.php?page=trimmomatic |
Java |
Window based |
yes |
yes |
no |
yes |
Can also remove adapters |
| SolexaQA |
1.13 |
sourceforge.net/projects/solexaqa/files/ |
Perl |
Window based (Running sum with -bwa option) |
no |
no |
yes |
no |
Cannot specify minimum read length to keep |
| Sickle |
1.2 |
github.com/ucdavis-bioinformatics/sickle |
C |
Window based |
yes |
yes |
no |
yes |
|
