@misc{10481/75141,
year = {2022},
month = {5},
url = {http://hdl.handle.net/10481/75141},
abstract = {The NCBI Sequence Read Archive currently hosts
microRNA sequencing data for over 800 different
species, evidencing the existence of a broad taxonomic
distribution in the field of small RNA research.
Simultaneously, the number of samples per
miRNA-seq study continues to increase resulting in
a vast amount of data that requires accurate, fast
and user-friendly analysis methods. Since the previous
release of sRNAtoolbox in 2019, 55 000 sRNAbench
jobs have been submitted which has motivated
many improvements in its usability and the
scope of the underlying annotation database. With
this update, users can upload an unlimited number
of samples or import them from Google Drive,
Dropbox or URLs. Micro- and small RNA profiling
can now be carried out using high-confidence Metazoan
and plant specific databases, MirGeneDB and
PmiREN respectively, together with genome assemblies
and libraries from 441 Ensembl species. The
new results page includes straightforward sample
annotation to allow downstream differential expression
analysis with sRNAde. Unassigned reads can
also be explored by means of a new tool that performsmapping
to microbial references, which can reveal
contamination events or biologically meaningful
findings as we describe in the example. sRNAtoolbox
is available at: https://arn.ugr.es/srnatoolbox/.},
organization = {European Commission	765492},
organization = {Spanish Government},
organization = {European Commission	AGL2017-88702-C2-2-R},
organization = {Chair 'Doctors Galera-Requena in cancer stem cell research'},
organization = {Stichting Cancer Center Amsterdam	CCA2021-9-77},
organization = {Tromsoforskningsstiftelse (TFS) ['MIRevolution']	20 SG BF},
organization = {TKI-Health Holland ['AQrate' project]},
publisher = {Oxford University Press},
title = {sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms},
doi = {10.1093/nar/gkac363},
author = {Aparicio Puerta, Ernesto and Giannoukakos, Stavros Panagiotis and Medina Casaubón, José María and García Moreno, Adrián and Carmona Sáez, Pedro and Marchal Corrales, Juan Antonio and Hackenberg, Michael},
}