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