f5c-v1.3

Changes/new features from f5c-v1.3-beta are:

1. adding a draft 5-mer pore model for upcoming RNA004 chemistry. To use this model:

   First download the model file

   wget https://raw.githubusercontent.com/hasindu2008/f5c/v1.3/test/rna004-models/rna004.nucleotide.5mer.model
   

   Then execute event align with --kmer-model pointing to the path to the downloaded k-mer model as follows:

   f5c eventalign --rna -b reads.bam -r reads.fastq -g transciptome.fa -o eventalign.tsv --kmer-model /path/to/rna004.nucleotide.5mer.model  # --slow5 
   reads.blow5  if using S/BLOW5 input
   

   Thanks @GoekeLab for help with this model generation and testing.

2. Fixing a bug that affected the last line of SAM output being truncated sometimes (--sam in eventalign).

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Compared f5c-v1.2, this f5c-v1.3 version (introduced in f5c-v1.3-beta) 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 (Note: As of this version signal samples corresponding to insertion are yet collapsed to the previous base. This will be improved in future versions). 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: