Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion

In this manuscript, we introduce and benchmark Mandalorion v4.1 for the identification and quantification of full-length transcriptome sequencing reads. It further improves upon the already strong performance of Mandalorion v3.6 used in the LRGASP consortium challenge. By processing real and simulat...

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Bibliographic Details
Published in:Genome Biology 2023-07, Vol.24 (1), p.167-15, Article 167
Main Authors: Volden, Roger, Schimke, Kayla D, Byrne, Ashley, Dubocanin, Danilo, Adams, Matthew, Vollmers, Christopher
Format: Article
Language:English
Subjects:
Annotations
Consortia
Datasets
Gene Expression Profiling
Gene loci
Genomes
High-Throughput Nucleotide Sequencing
Identification
Isoforms
Method
Performance evaluation
Protein Isoforms - genetics
Sequence Analysis, RNA
Transcriptome
Transcriptomes
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Summary:In this manuscript, we introduce and benchmark Mandalorion v4.1 for the identification and quantification of full-length transcriptome sequencing reads. It further improves upon the already strong performance of Mandalorion v3.6 used in the LRGASP consortium challenge. By processing real and simulated data, we show three main features of Mandalorion: first, Mandalorion-based isoform identification has very high precision and maintains high recall even in the absence of any genome annotation. Second, isoform read counts as quantified by Mandalorion show a high correlation with simulated read counts. Third, isoforms identified by Mandalorion closely reflect the full-length transcriptome sequencing data sets they are based on.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-023-02999-6