YSEQ Y-DNA Analysis Pipeline

Version

Current Version: 0.0.0

Overview

The YSEQ Y-DNA Analysis Pipeline is designed to process paired ended fastq.gz files and extract the Y- and MT-DNA Haplogroups.

Dependencies

• Python 3.6+

• Snakemake

• conda

• pandas

• Path

• bcftools

• samtools

• samtools

• tabix

Installation

1. Clone the repository:

   git clone https://github.com/morm24/yseq-pipeline.git
   cd yseq-pipeline

2. Install Python:

   apt install python3

3. Install snakemake:

   apt install snakemake

4. Install conda & mamba:

   Install and set up miniconda

   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
   bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
   conda config --set channel_priority strict

   Install mamba:

   conda install -n base -c conda-forge mamba

5. Install pandas & Path '''sh pip install Pandas Path '''

Usage

1. Prepare the input files:

   First Methode

   Add your sample

   Place your samples into the resources/sample/{SampleID} folder. The Filename name has to be: {SampleID}_R1.fastq.gz if paried end, the second files name must be {SampleID}_R2.fastq.gz

   Add the reference sequence

   Place the chosen reference sequence into resources/refseq/{ref}/{ref}.fa. The Name of the foldername and the fasta seqence have to be the same.

   add both to the samples.csv

   Add all SampleIDs to the file config/samples.csv. Separated with a "," state the name of the reference (file name without ending). Example:

   ID,REF
   63819,hs1
   

   configurate the settings

   Chose what type of reads you use, the mapping software and result directory in config/config.yaml

   Second Methode

   Add your resource folders

   Open config/config.yaml. Change the Sample, Reference and Results folders. Chose the read type, and mapping software.

   Add your sample

   Add all SampleIDs to the file config/samples.csv. Separated with a "," note the reference sequence, you want to map and analyze the sample to. Example:

   ID,REF
   63819,hs1
   

   configurate the settings

2. Run the pipeline: To just run the Pipeline, type the following command with the amount of cores it should use:

   snakemake -pfc {cores}

3. Check the output: TBD

Reference Sequences

Common reference sequences and their Download links are:

• hg38: Download hg38

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

• hg19: Download hg19

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz

• hs1: Download hs1

wget https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.fa.gz

YFull YTree Updates TO DO: change to free version

To download the latest YFull YTree updates, follow these steps:

1. Visit the YFull YTree website.
2. Download the latest JSON file from the resources section.
3. Place the downloaded JSON file in the resources/tree directory and rename it to latest_YFull_YTree.json.

Example

When set up corectly, and placed the hs1 sequence into resources/refseq/hs1/hs1.fa the following example workflow should run without errors and should take about 5 minutes to finish (faster with more cores): snakemake -pc 1

License

This project is licensed under the TBD License. See the LICENSE file for details.

Contact

For any questions or issues, please open an issue on the GitHub repository.

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