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.


To run DNAscent index, do:
   DNAscent index -f /path/to/fast5Directory
Required arguments are:
  -f,--files                path to fast5 files.
Optional arguments are:
  -o,--output               output file name (default is index.dnascent),
  -s,--sequencing-summary   path to sequencing summary file Guppy (optional but strongly recommended).

The only required input to DNAscent index is the full path to the top-level directory containing the sequencing run’s fast5 files, passed using the -f flag. This will typically be the directory created with MinKNOW during sequencing. An additional optional argument is the full path to the sequencing_summary.txt file, specified using the -s flag. This file is created by Guppy during basecalling and is located in the top level directory containing the Guppy-created fastq files. While including the sequencing summary file is optional, it is strongly recommended as it will make DNAscent index run much faster. 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.


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.