cauris_dotplot/run_dotplot.job at main · Snitkin-Lab-Umich/cauris_dotplot · GitHub

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#!/bin/bash

#SBATCH --mail-user=jjhale@umich.edu
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --export=ALL
#SBATCH --partition=standard
#SBATCH --account=esnitkin1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=5g
#SBATCH --time=05:00:00

module load Bioinformatics mummer/4.0.0rc1
module load R/4.4.0

# python dotplot.py --query query/MI_KPC_774/ \
# --subject reference/kpc_assemblies/MI_KPC_774_flye_medaka_polypolish.fasta \
# --name kpc_v1 --highlight highlight_data_KPC.tsv

#python sloop.py

# align to clade 1 reference
# python dotplot.py --query query/t40_illumina/ \
# --subject reference/b8441/B8441.fasta \
# --name ragtag_t40_illumina_v4

# python dotplot.py --query query/t40_hybrid/ \
# --subject reference/b8441/B8441.fasta \
# --name funqcd_t40_hybrid_v4


# align to clade 3 reference
# python dotplot.py --query /scratch/esnitkin_root/esnitkin0/jjhale/ragtag/output/t40_isolates_clade3/ \
# --subject query/t40_hybrid/UM_Caur_4.scaffolds.fa \
# --name ragtag_t40_illumina_clade3_v5

# python dotplot.py --query query/t40_hybrid/ \
# --subject query/t40_hybrid/UM_Caur_4.scaffolds.fa \
# --name funqcd_t40_hybrid_clade3_v5


# align to clade 4 reference
#python dotplot.py --query /scratch/esnitkin_root/esnitkin0/jjhale/ragtag/output/t40_isolates_clade4/ \
#--subject query/t40_hybrid/UM_Caur_10.scaffolds.fa \
#--name ragtag_t40_illumina_clade4_v6

#python dotplot.py --query query/t40_hybrid/ \
#--subject query/t40_hybrid/UM_Caur_10.scaffolds.fa \
#--name funqcd_t40_hybrid_clade4_v6

# ajay's samples
python dotplot.py --query query/Ajay_tpn/ \
--subject reference/b8441/B8441.fasta \
--name tpn_dotplots_v3 --highlight highlight_data_tpn_NAT.tsv