Scaffolding using long-read RNA?

nanoporetech / pinfish

Tools to annotate genomes using long read transcriptomics data

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Scaffolding using long-read RNA? #14

Closed andreaswallberg closed 4 years ago

andreaswallberg commented 4 years ago

Dear developers,

Any chance that this tool could be co-opted or extended to provide information about contig adjacency and scaffolding from split long-read RNA mappings?

Cheers!

bsipos commented 4 years ago

Since this tool depends on spliced alignments I don't think it is a good starting point for scaffolding. However one could map the reads to the scaffolds using minimap2 -ax map-ont and then parse the output looking for reads having secondary alignments on different contigs.

Cheers, Botond