摘要
Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.
基金
facility support from the Single-Molecule Sequencing Platform at Sun Yat-sen University Cancer Center.This work is supported by the National Natural Science Foundation of China(32070592 to JXY,32000395 to JL,82272789 to LZ)
Guangdong Basic and Applied Basic Research Foundation(2022A1515010717 and 2019A1515110762 to JXY and 2022A1515011873 to JL)
Guangdong Pearl River Talents Program(2019QN01Y183 to JXY,2021QN02Y168 to JL)
Guangzhou Municipal Science and Technology Bureau(202102020938 to JL)
Young Talents Program of Sun Yat-sen University Cancer Center(YTP-SYSUCC-0042 to JXY and YTP-SYSUCC-0040 to JL)。
