f5c-v1.3-beta

This beta version adds a new feature to f5c eventalign to write the output in PAF and SAM formats with signal-to-reference alignment information embedded as tags. This output is much more compact than the default TSV output, yet is sufficient for reconstructing the alignment. These SAM and PAF formats with signal alignment tags are the heart of the pileup view being implemented in Squigualiser.

• eventalign PAF output which is explained here (-c option)
• default eventalign SAM output changed (--sam option). The new SAM format is explained here. To revert to the old SAM format (same format as when Nanopolish --sam is provided), please provide --sam-out-version 1. The reason for the change in the SAM format is to support the upcoming pileup view in Squigualiser. See the screenshots below.
• -a shorthand option for --sam

DNA R10.4.1 pileup:

RNA R9.4.1 pileup: