RT Journal
A1 Keil, Netanya
A1 Monzó, Carolina
A1 McIntyre, Lauren
A1 Conesa, Ana
T1 Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
JF Genome Research 
JO Genome Research 
YR 2025 
FD April 01 
VO 35 
IS 4 
SP 987 
OP 998 
DO 10.1101/gr.280021.124 
UL http://genome.cshlp.org/content/35/4/987.abstract 
AB SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to develop a read-level quality control framework for replicated long-read RNA-seq experiments. The number and distribution of reads, as well as the number and distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories are informative of raw data quality. Multisample visualizations of QC metrics are presented by experimental design factors to identify outliers. We introduce new metrics for (1) the identification of potentially under-annotated genes and putative novel transcripts and for (2) quantifying variation in junction donors and acceptors. We applied SQANTI-reads to two different data sets, a Drosophila developmental experiment and a multiplatform data set from the LRGASP project and demonstrate that the tool effectively reveals the impact of read coverage on data quality, and readily identifies strong and weak splicing sites.