treeMarkET is a command-line wraper designed for extracting high quality SNPs from the forest tree species.
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Option #1 (recommended)
If you use conda you can install treeMarkET pre-requisited programs by running the following commands in your terminal:
conda config --add channels bioconda
conda create --name treeMarkET
conda activate treeMarkET
conda install -c bioconda trimmomatic samtools bcftools=1.15.1 bwa
Option #2
You can also use independatly install the following programs:
Download the wraper from this repository by:
git clone https://github.com/ulaszewski/treeMarkET.git
and
cd treeMarkET
chmod +x treeMarkET
Follow the installation instructions, run the script as shown below and answer the prompt questions
./treeMarkET
treeMarkET provides the user with several output files:
- clean fastq files
- mapped, filtered and indexed bam files
- raw and filtered maker files in *.bcf format
Please be advised that the generated files will be heavily using the your SSD/HDD up to 10x of the initial size of the input raw reads file(s). Please consider this factor while planning your reasearch.
In alphabetic order: Stephen Knobloch, Bagdevi Mishra, Marco Thines, Bartosz Ulaszewski, Stefan Wötzel
If you want to cite this pipeline as well as the reference please use this DOI: https://doi.org/10.3389/fgene.2021.691058 or directly:
Mishra, Bagdevi, et al. "A Chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat Content and distribution of SNPs." Frontiers in genetics 12 (2021).