index

DNAscent index is a DNAscent subprogram that creates a map between Oxford Nanopore readIDs and FAST5/POD5 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/directory
Required arguments are:\n"
   -f,--files                full path to fast5 or pod5 files.
Optional arguments are:\n"
   -s,--sequencing-summary   (legacy) path to sequencing summary file from using Guppy on fast5 files,
   -o,--output               output file name (default is index.dnascent).

The one required input to DNAscent index is the full path to the top-level directory containing the sequencing run’s FAST5 files or POD5 files (passed using the -f flag). It is permissible to pass a directory containing both FAST5 and POD5 files. We recommend passing data to DNAscent in POD5 format.

For users that are using legacy FAST5 format and Guppy, you can either:

• Pass only the FAST5 directory using the -f flag. DNAscent will iterate through each FAST5 file to build the index (expected to be slow).

• Pass the FAST5 directory using the -f flag and the sequencing_summary.txt file from Guppy using the -s flag. This will be 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.

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.