singleron-RD/accurascoperna is a bioinformatics pipeline for processing data from AccuraSCOPE RNA kit: low-throughput single cell 5' + 3' RNA .
In brief, the workflow does the following:
- Read QC (
FastQC) - Demultiplexing 3' and 5' reads; convert 5' barcode to 3' barcode; generate STARSolo command-line arguments (
convert.py) - Filter gtf attributes (
filter_gtf.py) - Generate star genome Index (
STAR) - Mapping and quantification of 3' reads. (
STARSolo) - Mapping and quantification of 3' read + 5' reads. (
STARSolo) - HTML report (
MultiQC)
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.