R package for down-stream processing of nanoranger output.
The package provides capabilities to read out single nucleotide variants, insertions/deletions, fusion genes/CAR sequences and isoforms from amplicons sequenced with long-read sequencing with the nanoranger protocol.
By using starcode, UMIs that arise due to sequencing error are collapsed in groups within a Levenshtein distance of 3. This is a strategy to deal with the issue that UMIs in 10x Genomics libraries - as opposed to cell barcodes - do not have a whitelist that can be used for correcting sequencing error.
For vignettes on how to use this package see here
knee_plot(): plot knee plot to identify optimal cutoff for cells
extract_mutation(): extraction of single nucleotide variants
extract_indel(): extraction of insertions or deletions with specific length
extract_length_diff(): detect truncated transcripts
extract_fusion_gene(): extraction of fusion genes or CAR sequences
extract_isoforms(): extraction of differentially spliced exons
devtools::install_github('liviuspenter/nanoranger.R')