TY - JOUR
T1 - SQANTI
T2 - Extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
AU - Tardaguila, Manuel
AU - De La Fuente, Lorena
AU - Marti, Cristina
AU - Pereira, Cécile
AU - Pardo-Palacios, Francisco Jose
AU - Del Risco, Hector
AU - Ferrell, Marc
AU - Mellado, Maravillas
AU - Macchietto, Marissa
AU - Verheggen, Kenneth
AU - Edelmann, Mariola
AU - Ezkurdia, Iakes
AU - Vazquez, Jesus
AU - Tress, Michael
AU - Mortazavi, Ali
AU - Martens, Lennart
AU - Rodriguez-Navarro, Susana
AU - Moreno-Manzano, Victoria
AU - Conesa, Ana
N1 - Publisher Copyright:
© 2018 Tardaguila et al.
PY - 2018/3
Y1 - 2018/3
N2 - High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.
AB - High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.
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U2 - 10.1101/gr.222976.117
DO - 10.1101/gr.222976.117
M3 - Article
C2 - 29440222
AN - SCOPUS:85046109578
SN - 1088-9051
VL - 28
SP - 396
EP - 411
JO - Genome research
JF - Genome research
IS - 3
ER -