samtools_indexing.pbs

#!/bin/bash
#PBS -q condo05
#PBS -l select=1:ncpus=64:mem=500GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N samtoolsFun

cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly/pre_alignment_scaffolding

#1. indexing of the fasta scaffolding file 

module load samtools

#samtools faidx /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly/yahs_scaffolding/yahs.out_scaffolds_final.fa


#indexed file is saved in the folder where the fasta file is located

#2. printing the first two columns into a new file and generating the genome file 

cut -f1,2 yahs.out_scaffolds_final.fa.fai > scaffolding.genome