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Circlator.sh
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# linkage
http://sanger-pathogens.github.io/circlator/
# load module
module load bwa/0.7.17
module load prodigal/2.6.3
module load samtools/1.2
module load mummer/3.23
module load perl/5.20.1
module load java/8u151
module load canu/1.7
module load spades/3.9.0
module load python/3.5.2
cd ~
. mypython3env/bin/activate
# for installation
pip3 install circlator
# cd to working directory
cd /srv/scratch/z5039045/PacBio/2018-06-07_circlator
# combine all subreads together
cat /srv/scratch/z3452659/ThomasPacBio-Nov15/data/2015-11-23.PacBioRaw/SON1053*/SON1053*/*.subreads.fasta > combined_all_subreads.fasta
# copy assemblies to working directory
cp /srv/scratch/z5039045/PacBio/SON1053.SP16554.hcq.qv20.fas .
# run circlator
circlator all hcq7.fasta combined_all_subreads.fasta hcq7_circularized
circlator all hcq43.fasta combined_all_subreads.fasta hcq43_circularized
circlator all hcq44.fasta combined_all_subreads.fasta hcq44_circularized
# for other checks
# get sequence length
cd /srv/scratch/z5039045/PacBio
perl /srv/scratch/z5039045/Scripts/get_fasta_stats.pl SON1053.SP16554.hcq.qv20.fas
# hcq7_SON1053__SP016554.7 3690170 57.0% 0
cd /srv/scratch/z5039045/PacBio/quiver_polish
perl /srv/scratch/z5039045/Scripts/get_fasta_stats.pl combined_10.fasta
# Ratl_SON1053__RE16554.7 3662281 57.1% 0
perl /srv/scratch/z5039045/Scripts/get_fasta_stats.pl combined_10.consensus.fasta
# Ratl_SON1053__RE16554.7 3662295 57.1% 0