Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing.

ABSTRACT:

Motivation

Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes.

Results

We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read sequencing data of full-length single-cell or single-nuclei cDNA. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessm

SUBMITTER: De Rijk P 

PROVIDER: S-EPMC11419950 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature