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beechMarkET is a command-line wraper designed for extracting high quality SNPs from the common beech (Fagus sylvatica L.) genome.
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Option #1 (recommended)
If you use conda you can install beechMarkET pre-requisited programs by running the following commands in your terminal:
conda config --add channels bioconda
conda create --name beechmarket
conda activate beechmarket
conda install -c bioconda trimmomatic samtools bcftools=1.15.1 bwa
Option #2
You can also use independatly install the following programs:
Option #3
Dokcer image (in preparation)
Download the reference genome of Fagus sylvatica from the Thines Lab site or from NCBI Genome repository. If needed unzip the assembly and index it with the following command:
bwa index -a is your_reference_name.fasta
samtools faidx your_reference_name.fasta
Download the wraper from this repository by:
git clone https://github.com/ulaszewski/beechMarkET.git
and
cd beechMarkET
chmod +x beechmarket*
Follow the installation instructions, run the script as shown below and answer the prompt questions
./beechmarket
OR
./beechmarket_module-name
beechMarkET 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).