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Can I read Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison on EtoBox?
Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison by Kuijpers, Lucas (author);Hornung, Bastian (author);van den Hout - van Vroonhoven, Mirjam C. G. N. (author);van IJcken, Wilfred F. J. (author);Grosveld, Frank (author);Mulugeta, Eskeatnaf (author) is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison about?
## Background Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used. ## Results We show that STARsolo, splitpip
Who reads Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- Kuijpers, Lucas (author);Hornung, Bastian (author);van den Hout - van Vroonhoven, Mirjam C. G. N. (author);van IJcken, Wilfred F. J. (author);Grosveld, Frank (author);Mulugeta, Eskeatnaf (author)
- Publisher
- Springer Science and Business Media LLC
- Published
- 2024
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)