lycaeides_sv

Directory for whole genome paired end reads: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/whole_genomes/sequences

In this directory I used the 3kb files.

Directory for alignments and variant calling: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lyc_sv

Directory for the new PacBio corrected genome: /uufs/chpc.utah.edu/common/home/gompert-group3/data/LmelGenome/Lmel_dovetailPacBio_genome.fasta

Doing Aligntments:

Directory: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lyc_sv/Alignments

• 1. Used the paired end sequences to do alignment to the dovetail melissa genome using bwa mem. Here the script is modified to align paired end reads. Used the script wrap_qsub_slurm_bwa_mem.pl for alignments using bwa. This file created the sam files.

  2. Converted sam files to bam files using the script wrap_qsub_slurm_sam2bam.pl.

  3. These are files aligned to the new genome.

  4. I then copied these sorted bam files with their indexes to the sv-callers/snakemake/data_lyc/bam folder.

Variant calling using sv-callers:

Directory: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lyc_sv/Variantcalling

source acitvate wf

cd snakemake

Then edit the analysis_lyc.yaml and Snakefile to make sure all the paths and everything are set.

For running snakemake:

The cluster specifications are in cluster.yaml file.

To submit Snakemake jobs use run_workflow.sh and execute from command line as ./run_workflow.sh

This will submit all the jobs in parallel to the cluster.