HOWTOTettelin.txt

# lines can be commented out with a leading '#'

# 1.0) download genomes in GenBank format from NCBI FTP site
cd test_Streptococcus
../download_genomes_ncbi.pl test_Streptococcus_download_list.txt
cd ..

# 1.1) run BLAST jobs with 4 CPU cores and optionally HMMER 
./get_homologues.pl -d test_Streptococcus/ -n 4 -o
./get_homologues.pl -d test_Streptococcus/ -n 4 -D -o

# 1.2) calculate core-genomes with all BDBH, OMCL & COG algorithms
./get_homologues.pl -d test_Streptococcus/ 
./get_homologues.pl -d test_Streptococcus/ -M
./get_homologues.pl -d test_Streptococcus/ -G
./get_homologues.pl -d test_Streptococcus/ -M -D

# 1.3) calculate consensus core-genome with syntenic genes
./compare_clusters.pl -s -n -o test_Streptococcus_intersection -d \
test_Streptococcus_homologues/S_f0_alltaxa_algCOG_e0_,\
test_Streptococcus_homologues/S_f0_alltaxa_algOMCL_e0_,\
test_Streptococcus_homologues/S_f0_alltaxa_algBDBH_e0_

# 1.4) calculate core-genome with coverage and identity as in the Tettelin paper (cover=50%,%ID=50)
./get_homologues.pl -d test_Streptococcus/ -M -C 50 -S 50

# 1.6) calculate core intergenic clusters
./get_homologues.pl -d test_Streptococcus/ -g

# 1.7) estimate and plot core- and pangenome sizes with all BDBH, OMCL & COG algorithms
./get_homologues.pl -d test_Streptococcus/ -c
./get_homologues.pl -d test_Streptococcus/ -M -c
./get_homologues.pl -d test_Streptococcus/ -G -c

# 1.8) calculate core-genome of genomic features based on nucleotide similarity (BLASTN)
./get_homologues.pl -d test_Streptococcus/ -n 4 -a CDS,rRNA,tRNA


# 2.1) calculate pan-genome with OMCL & COG algorithms
./get_homologues.pl -d test_Streptococcus/ -M -t 0
./get_homologues.pl -d test_Streptococcus/ -G -t 0

# 2.2) build consensus pangenomic matrix
./compare_clusters.pl -d test_Streptococcus_homologues/S_f0_0taxa_algCOG_e0_,\
test_Streptococcus_homologues/S_f0_0taxa_algOMCL_e0_ -m -T -o test_Streptococcus_intersection

# 2.3) plot pangenomic compartments and estimate core- and pan-genome size with mixture models
./parse_pangenome_matrix.pl -m test_Streptococcus_intersection/pangenome_matrix_t0.tab -s

# 2.4) check accesory genes present in A genomes and absent in B
./parse_pangenome_matrix.pl -m test_Streptococcus_intersection/pangenome_matrix_t0.tab \
	-A test_Streptococcus/A.list -B test_Streptococcus/B.list -g -e