rDNA_variant_caller

Repository to call rDNA variants from short read sequencing

Software dependencies

Package	Version
MUMMER	4.0.0rc1
ANACONDA	2023.07
seqkit	2.8.0
Samtools	1.19.2
bwa	0.7.17
gatk	4.5.0.0
java-openjdk	17.0.11+9
bcftools	1.19
R	4.3.2

We created a singularity image with all necessary software

singularity pull library://jmiguelramirez/jmiguelramirez/rdna_variant_caller

Running the code

To run the code sequentially

./Pipeline.sh -h
This code runs a variant caller for rDNA reads

Syntax: Pipeline.sh [-h|-t|-n|-f|-i|-o]
parameters:
h     Print the help message.
t     Type of input data: Either DNA or RNA.
n     Basename of the input data: (e.g., for a bam file named sample.bam: -n sample, for fastqs named sample_1.fastq.gz and sample_2.fasq.gz: -n sample. This means that paired fastqs should end by _1.fastq.gz and _2.fastq.gz)
f     Type of input data format: Either bam (for bam/cram/sam) or fastq.
i     Input folder.
o     Output folder.

Example using a small fraction of reads from a sample in the publicly available dataset: Randolph et al. Science 2021

./Pipeline.sh -t DNA -n SRR14773542 -f fastq -i Data/ -o Results/

If using the singularity image:

singularity exec --bind workspace/ ./Pipeline.sh -t DNA -n SRR14773542 -f fastq -i Data/ -o Results/

To run the code in a parallel manner, check inside Scripts_parallel/