################################# GUIDE TO RUN THE SCRIPT getLCA.py #################################
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Download the NCBI taxonomy files, names.dmp and nodes.dmp
mkdir taxdump wget ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz tar -xzf taxdump.tar.gz -C taxdump rm taxdump.tar.gz
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Update the paths to names.dmp and nodes.dmp on line 3 and 4 in the script get_LCA_functions.py
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Map reads to DB using bowtie (or a mapper of your choice) - see Prepare_ref_DB_guide.md
bowtie2 -k 500 -p 24 -f -x $DB -U $infile --no-unal > $filename.unsorted.sam
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Sort samfile
sort -k1 $filename.unsorted.sam > $filename.sam rm $filename.unsorted.sam
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Assign LCA
python get_LCA.py $filename.sam
OPTIONAL: 6) Report a sorted list of vertebrate species assigned below family level:
cat $filename.getLCA|grep -v 'NOMATCH'|grep 'genus\|family\|species\|subfamily\|subspecies\|subgenus'|grep 'Vertebrata'|awk '{print $2}'|sort|uniq -c|sort -nk1|awk -F ':' '{print $1}'