Here are the basic steps for doing the Pseudomonas analysis using Nullarbor.
By Emily Richardson.
# make project directory
mkdir 2016_10_21_Pseud
cd 2016_10_21_Pseud
#click on view project xml
http://www.ebi.ac.uk/ena/data/view/PRJEB6515&display=xml
#Select the link for the reads
http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=PRJEB6515&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes
#edit this link to only request submitted_field
http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=PRJEB6515&result=read_run&fields=submitted_ftp
#Change name to somthing more meanginful
mv filereport\?accession=PRJEB6515\&result=read_run\&fields=submitted_ftp.1 read_locations.txt
# replace the semi colon with a new line
tr ';' '\n' < read_locations.txt > reads.txt
# get the subset you require from
wget "http://147.188.173.140/public/researcher/cc17_subset.txt"
# get the subset from reads.txt
grep -f cc17_subset.txt reads.txt > cc17_reads.txt
download these reads
wget -i cc17_reads.txt
# make directory for your reads
mkdir reads
#move all reads to reads folder
mv *gz reads
# get the reference PAO1 Pseduomonas Aeruginosa
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/archi
ve/old_refseq/Bacteria/Pseudomonas_aeruginosa_PAO1_uid57945/NC_002516.gbk
# This is the command to make your nullarbor input file
# EMILY BREAK THIS DOWN
cd reads
for read1 in *R1*gz ; do printf "${read1%_R1*}\treads/${read1}\treads/${read1%_R1*}_R2_paired.fastq.gz\n" ; done > ../cc17_samples.tab
cd ../
nullarbor.pl --name cc17_pseud --mlst paeruginosa --ref NC_002516.gbk --input cc17_samples.tab --outdir cc17_pseud_nullarbor
nice make -j 1 -C /home/ubuntu/2016_10_21_Pseud/cc17_pseud_nullarbor
# Run nullarbour MAKE SURE YOU ARE IN A SCREEN!!!