Class data:

• GCF_000005845.2_ASM584v2_genomic.fna - genome assembly
• SRR2584863_1.fastq - fastq sequence file, paired-1
• SRR2584863_2.fastq - fastq sequence file, paired-2
• *.smk - snakemake files
• config_variant.yml - configuration file
• submit_snakemake.sh - sample slurm file

Run interactively - good for testing

ijob -c 1 -A allocation -p interactive –v -t 2:00:00

Modules

module spider <package>

• specifics and version of package available

module spider snakemake
module load snakemake/9.8.1
module list
snakemake -help

Other modules needed

module load bwa/0.7.17
module load  cutadapt/4.9
module load snakemake/9.8.1
module load freebayes/1.3.10
module load  samtools/1.21

Running snakemake - genome alignment

Snakefile - file.smk, contains rules for snakemake

snakemake -c 1 -s align.smk
- --dry-run -np good to test first without producing output
- -n only show steps, don't run, -p print shell commands
- -c number of cores
- -s needed if using a named snakefile (if just called "snakefile",  don't need the –s flag)

snakemake --dag| dot -Tpng > dag_align.png

Running snakemake - variant detection

Snakefile - file.smk, contains rules for snakemake

snakemake -c 1 -s variant-call.smk
- --dry-run
- -c number of cores
- -s needed if using a named snakefile (if just called "snakefile", don't need)

snakemake --dag -s variant-call.smk | dot -Tpng > dag_variant.png