index

DNAscent index is a DNAscent subprogram that creates a map between Oxford Nanopore readIDs and fast5 files. This allows DNAscent detect to scan through bam files and pull out the relevant signal information for each read.

Usage

To run DNAscent index, do:
   DNAscent index -f /path/to/fast5Directory
Required arguments are:
  -f,--files                path to fast5 files,
  -s,--sequencing-summary   path to sequencing summary file Guppy.
Optional arguments are:
  -o,--output               output file name (default is index.dnascent),
     --GridION              account for the different sequencing summary format used by in-built GridION basecalling.

The required inputs to DNAscent index are the full path to the top-level directory containing the sequencing run’s fast5 files (passed using the -f flag) and the sequencing_summary.txt file from Guppy (located in the top-level Guppy output directory). Note that the sequencing_summary.txt file created by onboard GridION basecalling has a slightly different format from that of the summary file generated by Guppy, and this can be accounted for with the --GridION flag. The default behaviour of DNAscent index is to place a file called index.dnascent in the working directory. The name of this file can be overridden using the -o flag.

Output

DNAscent index will put a file called index.dnascent in the current working directory (note that if you used the -o flag, then the file will have the name and location that you specified). This file will be needed as an input to DNAscent detect.