Hi Dear colleagues

I've got a FASTQ file that is produced using Thermofisher Ion S5 machine, I want to analyze this raw data using NIPTMer software:

Main article: Article NIPTmer: Rapid k-mer-based software package for detection of...

Download link: http://bioinfo.ut.ee/NIPTMer/programs/

Help: http://bioinfo.ut.ee/NIPTMer/readme.txt

This software package has a directory named "list" that the files in the dir are named look like this pattern: "CHID_cleaned_25.list" which CHID is chromosome ID.

For analyzing the raw data this app has three steps:

A. Create reference kmer lists (to be run once before analysis)

B. Create control dataset

C. Analyze samples

The problem is here, should I do the first step again? because we have the data directory, and in step B we need FASTQ file.

I just want to make a k-mer list using raw FASTQ data file that belongs to the patients, using glistmaker and then calculate k-mer counts using make_table.pl script. And finally analyze them using ZandMah python script.

Would you please help me with the corrent work flow of this software?