Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing

Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package called scywalker.

Type: Transcriptome Analysis
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000768	Dataset for the manuscript Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing. Contains fastq files for 4 brain samples obtained from short-read NovaSeq 6000 v1.5 Illumina and long-read Oxford Nanopore PromethION sequencing. Single-cell suspensions were generated using 10x Genomics Chromium Next GEM Single Cell 3'Kit v3.1	Illumina NovaSeq 6000 PromethION	8

Publications	Citations
Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing. De Rijk P, Watzeels T, Küçükali F, Van Dongen J, Faura J, Willems P, De Deyn L, Duchateau L, Grones C, Eekhout T, De Pooter T, Joris G, Rombauts S, De Rybel B, Rademakers R, Van Breusegem F, Strazisar M, Sleegers K, De Coster W. Bioinformatics 40: 2024 btae549	0