srun -t 1440 -n 1 --mem 8000 --reservation workshop --pty /bin/bash

wget --no-check-certificate ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/PhiX/Illumina/RTA/PhiX_Illumina_RTA.tar.gz
curl -k https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/pdhqicmfgw2bra8/variant.neighborhoods.fa > regions.fa
   
grep ">" regions.fa | cut -c 2-
grep ">" regions.fa | cut -c 2- | cut -f1 -d:
grep ">" regions.fa | cut -c 2- | cut -f1 -d: | sort
grep ">" regions.fa | cut -c 2- | cut -f1 -d: | sort | uniq -c
grep ">" regions.fa | cut -c 2- | cut -f1 -d: | sort | uniq -c | sort -rn -k1,1

ln -s PhiX/Illumina/RTA/Sequence/WholeGenomeFasta/genome.fa .

bwa mem genome.fa regions.fa 1> aln.sam 2> aln.err

grep ">" regions.fa | cut -c2- | while read header; do echo "contig_$header" >> b; done