Software |
Interface1
|
Type |
Target group |
ITS
extraction |
Unique features |
Reference |
QIIME2 |
graphical, CL |
offline, multiple included dependencies |
prokaryote, short-read |
ITSxpress |
interactive data visualisation;
Deblur filtering |
Bolyen et al., 2019 |
mothur |
CL |
offline |
prokaryote, short-read |
- |
OptiClust
clustering |
Schloss, 2020 |
Claident |
CL |
offline |
universal, short-read |
ITSx |
noise removal
options |
Tanabe & Toju, 2013 |
PIPITS |
CL |
offline |
fungi, ITS1, ITS2 |
ITSx |
- |
Gweon et al.,
2015 |
SEED2 |
graphical |
offline |
universal, short-read |
ITSx compatible |
read visualisation |
Vetrovsky et al., 2018 |
PEMA |
CL |
offline, multiple included dependencies |
universal,
short-read |
- |
parameter file for automated pipeline |
Zafeiropoulos
et al., 2020 |
PipeCraft |
graphical |
offline, multiple included dependencies |
universal, short/long-read |
ITSx |
multiple HTS platform- and
data-specific options |
Anslan et al., 2017 |
DADA2 |
CL (R-Studio) |
offline |
universal, short/long-read |
- |
ASV
calculation |
Callahan et al., 2016 |
LOTUS2 |
CL |
offline |
universal, short/long-read |
ITSx |
low RAM
usage, false positives removal, |
Hildebrand et al., 2014 |
Galaxy |
graphical |
online |
prokaryote, short-read |
- |
links to
other Galaxy functions |
Jalili et al., 2020 |
FROGS |
graphical |
online |
prokaryote, short-read |
ITSx |
Galaxy
functions |
Escudie et al., 2018 |
AMPtk |
CL |
offline |
universal, short-read |
- |
hybrid method for
taxonomy assignment; spike-in control |
Palmer et al.,
2018 |
OBITools |
CL |
offline |
universal, short-read |
- |
- |
Boyer et al.,
2016 |
SCATA |
graphical |
online |
fungi, short/long-read |
ITSx |
unique
clustering options |
https://scata.mykopat.slu.se/ |
gDAT |
graphical |
offline |
universal, short-read |
- |
- |
Vasar et
al., 2021 |
Cascabel |
CL |
offline |
universal, short-read |
- |
graphical report- |
Abdala Asbun et al., 2020 |
MICCA |
CL |
offline |
universal, short-read |
- |
OTUCLUST clustering
algorithm |
Albanese et al., 2015 |
SWARM |
CL |
offline |
universal, short-read |
- |
local single-linkage
clustering |
Mahe et al., 2021 |
CloVR-ITS |
CL |
offline/online |
fungi, short-read |
- |
Virtual
machine-based with the possibility to run on Amazon EC2 Cloud |
White et
al., 2013 |
DAnIEL |
graphical |
online |
fungi, short-read |
ITSx (via PIPITS) |
raw data download from SRA |
Loos et al., 2021 |