Repository to call rDNA variants from short read sequencing
| 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
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/