kam (Kmer Analysis Modules)

This is a collection of tools written as part of a pipeline for Kmer based variant detection.

Docker

From dockerhub

docker pull trentzz/kam

From repo

Start by cloning this repo, then.

cd kam
docker build -t kam .
docker run -it --rm kam bash

You should now have access to the tools below, as well as jellyfish and km.

Tools

Tool	Description
multiseqex	MULTI SEQuence EXtraction. Batch process extracting sequences from a reference file. Similar to samtools faidx but multi-core.
kmtools	Extension tools for km including multithreading, filtering, stats, and plotting.
refolder	CLI that moves files matching a glob pattern into an equal number of subfolders.
vcf2pandas	vcf2pandas is a python package to convert vcf files to pandas dataframes.
vcf2xlsx	vcf2xlsx is a python cli package to convert vcf files to excel files.

Workflow

You have a few options for using all the tools here and running a workflow:

1. Simple bash script: example-workflow.sh
2. Nextflow script: example-workflow.nf
3. Manually running each tool individually. This is useful when using a custom workflow, debugging, rerunning certain sections, etc.

Bash Script

Nextflow

Manually