Quick Start¶

This is a quick start guide to use KCFtools for genomic variation analysis. It covers installation, database preparation, and basic usage. We recommend reading the Workflow and Methodology sections for a more detailed understanding of the tool's functionalities.

1. Install KCFtools¶

Assuming the prerequisites are met, you can install KCFtools using the following command:

$ conda install -c bioconda kcftools

2. Prepare KMC Database¶

Ensure you have a KMC database ready. If you don't have one, you can create it using KMC3:

$ kmc -k31 -ci1 -cs10000 -fm -t4 @reads.txt sample1_kmc tmp/

• @reads.txt contains a list of input FASTQ files.
• Output will be sample1_kmc.kmc_pre and sample1_kmc.kmc_suf.

3. Create variations KCF file¶

To create a KCF file containing variations, use the getVariations command:

$ kcftools getVariations \
    --kmc sample.kmc_db \
    --reference reference.fasta \
    --sample sample \
    --output sample.kcf \
    --window 10000 \
    --feature window \
    --memory \
    --threads 2

This command will generate a KCF file named sample.kcf containing the variations detected between the reference genome and the sample KMC DB.

4. Find IBS windows¶

To identify IBS (Identity by State) windows, use the findIBS command:

$ kcftools findIBS \
    --input sample.kcf \
    --output sample.ibs \
    --summary

This command will generate an IBS summary file named sample.ibs.summary.tsv containing the IBS windows identified in the KCF file with additional summary.