diff --git a/recipe/bin/plot_circos b/recipe/bin/plot_circos
index 216f774..d4f9f6a 100644
--- a/recipe/bin/plot_circos
+++ b/recipe/bin/plot_circos
@@ -1,402 +1,95 @@
 #!/bin/bash
-
 # Simple script to create a circos plot between two FASTA files.
 
+######################
+### Get script DIR ###
+######################
+export SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+
 ############
 ### Help ###
 ############
-Help()
-{
-cat << EOF
-
-Simple script to create a circos plot between two FASTA files.
-Copyright, Felipe Almeida <almeidafmarques@outlook.com>, 2021
-
- Syntax: plot_circos.sh [-h] [--fofn <file> --outdir <outdir> --minlen <int> --minid <int>
-                              --linklen <int> --show_intrachr --gc_window <int> --gc_step <int>
-                              --labels <file> ]
-
- Options:
-
- # Help
- -h/--help                           Print this help
-
- # Output
- --outdir                            Path to output directory [Default: ./results]
-
- # Input file of file names
- # CSV: fasta path,prefix,color
- --fofn                              File of file names contatining list of fastas to
-                                     draw circos plot.
-
- # Input min. length
- --minlen                            Min size of contigs to consider for plot [Default: 10000]
-
- # Links (blastn) min. percentage id
- --minid                             Min. percentage id to filter the results of blastn to draw links [Default: 85]
- --linklen                           Min. link (blastn hit) length to display in plot [Default: 5000]
- --show_intrachr                     Tells the program to create a conf file showing intra chr links [Default: false]
-                                     Mandatory if using only one FASTA, otherwise, links will not be shown.
-
- # GC skew config
- --gc_window                         GC skew window size [Default: 5000]
- --gc_step                           GC skew step size [Default: 5000]
-
- # Labels config
- --labels                            TSV file containing the label definitions for plotting. The file must contain
-                                     3 or 4 columns as shown at http://circos.ca/documentation/tutorials/2d_tracks/text_1/lesson,
-                                     "DATA FORMAT" section. The first column must be the name (ID) of the contig.
-
-
-EOF
-}
+source ${SCRIPT_DIR}/../src/help.sh
 
 ################
 ### Defaults ###
 ################
-RESULTS="./results" # tmp directory
-FOFN=""
-LABELS=""
-LABEL_CONF=""
-FASTA=""
-FASTA_PREFIX=""
-FASTA_COLOR=""
-MINLEN=10000
-MINID=85
-MINLINKLEN=5000
-INTRACHR_FILE="links_concatenated_colored_no_intrachr.txt"
-INTRACHR_SHOW="no"
-GCWINDOW=5000
-GCSTEP=5000
+export THREADS=1
+export RESULTS="./results"
+export FOFN=""
+export LABELS=""
+export LABELS_CONF=""
+export TILES=""
+export TILES_CONF=""
+export FASTA=""
+export FASTA_PREFIX=""
+export FASTA_COLOR=""
+export MINLEN=10000
+export MINID=85
+export MINLINKLEN=5000
+export INTRACHR_FILE="links_concatenated_colored_no_intrachr.txt"
+export INTRACHR_SHOW="no"
+export GCWINDOW=5000
+export GCSTEP=5000
 
 ######################################
 ### Function to filter FASTA files ###
 ######################################
-filter()
-{
-# create results dir
-mkdir -p $RESULTS
-
-# create dir for files
-mkdir -p ${RESULTS}/filtered
-
-# filter genomes
-IFS=','
-while read -r FASTA FASTA_PREFIX FASTA_COLOR ; do
-  name="$(basename $FASTA)" ;
-  $CONDA_PREFIX/bin/perl $CONDA_PREFIX/bin/removesmalls.pl $MINLEN $FASTA >> ${RESULTS}/filtered/"$name" ;
-  continue
-done<"$FOFN"
-
-}
+source ${SCRIPT_DIR}/../src/filter.sh
 
 ##########################################
 ### Function to create karyotype files ###
 ##########################################
-karyotype()
-{
-# create dir
-mkdir -p ${RESULTS}/conf
-
-# write karyotypes
-IFS=','
-while read -r FASTA FASTA_PREFIX FASTA_COLOR ; do
-  name="$(basename $FASTA)" ;
-  FILTERED_FASTA=${RESULTS}/filtered/"$name" ;
-  bioawk -c fastx -v p=$FASTA_PREFIX -v color=$FASTA_COLOR \
-    '{ printf "chr - " substr($name,1) " " p":" substr($name,1) " " "0" " " length($seq) " " color"\n" }' \
-    $FILTERED_FASTA >> ${RESULTS}/conf/circos.sequences.txt ;
-done<"$FOFN"
-}
+source ${SCRIPT_DIR}/../src/karyotypes.sh
 
 #############################################
 ### Function to find links between fastas ###
 #############################################
-find_links()
-{
-# create dir
-mkdir -p ${RESULTS}/all_vs_all_blast
-
-# concatenate genomes
-cat ${RESULTS}/filtered/* >> ${RESULTS}/all_vs_all_blast/concatenated_genomes.fasta ;
-export CONCAT_FASTA=${RESULTS}/all_vs_all_blast/concatenated_genomes.fasta
-export BLAST_DB=${RESULTS}/all_vs_all_blast/blast_db
-
-# Run blast
-makeblastdb -in $CONCAT_FASTA -dbtype nucl -out $BLAST_DB &> /dev/null ;
-blastn -task blastn -perc_identity $MINID -query $CONCAT_FASTA -db $BLAST_DB \
-    -outfmt "6 qseqid qstart qend sseqid sstart send pident length mismatch gapopen evalue bitscore stitle" \
-    -out ${RESULTS}/all_vs_all_blast/tmp.blast
-
-# Filter blast
-awk -F '\t' -v minid=$MINID '{ if ($7 >= minid) { print } }' ${RESULTS}/all_vs_all_blast/tmp.blast > ${RESULTS}/all_vs_all_blast/all_vs_all.blast
-
-# Remove tmp
-rm ${RESULTS}/all_vs_all_blast/tmp.blast
-}
+source ${SCRIPT_DIR}/../src/find_links.sh
 
 #########################################################################
 ### Function to parse blastn (links) and create conf file with colors ###
 #########################################################################
-parse_links()
-{
-# create dir
-mkdir -p ${RESULTS}/conf
-
-# Filter blocks with more then N bp hits
-awk -v minlen=$MINLINKLEN '{ if ($8 >= minlen) { print } }' \
-  ${RESULTS}/all_vs_all_blast/all_vs_all.blast | cut -f 1,2,3,4,5,6 >> ${RESULTS}/conf/links_concatenated.txt ;
-
-# get links comming from contigs and give it colors
-IFS=','
-while read -r FASTA FASTA_PREFIX FASTA_COLOR ; do
-  bioawk -c fastx '{ printf $name"\n" }' $FASTA > tmp_names.fasta ;
-  awk -v color1=$FASTA_COLOR -F'\t' 'NR==FNR{c[$1]++;next};c[$1] > 0 {print $0 "\t" "color="color1}' \
-    tmp_names.fasta ${RESULTS}/conf/links_concatenated.txt >> ${RESULTS}/conf/links_concatenated_colored.txt
-  rm tmp_names.fasta ;
-done<"$FOFN"
-
-# create additional file whithout intrachr links
-awk -F'\t' '{ if ($1 != $4) { print } }' ${RESULTS}/conf/links_concatenated_colored.txt > ${RESULTS}/conf/links_concatenated_colored_no_intrachr.txt ;
-}
+source ${SCRIPT_DIR}/../src/parse_links.sh
 
 #############################################################################
 ### Function to sort and remove duplicates from links and karyotype files ###
 #############################################################################
-dedup()
-{
-for file in $(ls ${RESULTS}/conf/*); do
-    sort -u $file > tmp.txt ;
-    cat tmp.txt > $file ;
-    rm tmp.txt
-done
-}
+source ${SCRIPT_DIR}/../src/dedup.sh
 
 ###############################################
 ### Function to check which chrs have links ###
 ###############################################
-check_links()
-{
-# get chrs with links
-## chr source
-cut -f 1 ${RESULTS}/conf/links_concatenated_colored.txt >> tmp.chrs
-## chr target
-cut -f 4 ${RESULTS}/conf/links_concatenated_colored.txt >> tmp.chrs
-
-# export LINE
-CHRS=$(cat tmp.chrs | sort -u | tr '\n' ';') ;
-rm tmp.chrs ;
-export CUSTOM_CHR_LINE="chromosomes = "${CHRS} ;
-}
+source ${SCRIPT_DIR}/../src/check_links.sh
 
 #########################################################
 ### Function to create GC skew file proper for Circos ###
 #########################################################
-gc_skew()
-{
-# exec GCcalc.py
-$CONDA_PREFIX/bin/python3 $CONDA_PREFIX/bin/GCcalc.py -f ${RESULTS}/all_vs_all_blast/concatenated_genomes.fasta -w $GCWINDOW -s $GCSTEP | \
-    cut -f 1,2,3,5 | awk '{ if ($4 > 0) print $0 "\t" "color=dblue"; else print $0 "\t" "color=red"}' > ${RESULTS}/conf/GC_skew.txt
-}
-
-##################################################
-### Function to create feature labels from GFF ###
-##################################################
-gff2labels()
-{
-# load variable
-read -r -d '' LABEL_CONF << EOM
-# Labels
-<plot>
-label_snuggle    = yes
-type             = text
-color            = black
-file             = feature_labels.txt
-
-r0 = 1r
-r1 = 1r+200p
+source ${SCRIPT_DIR}/../src/gc_skew.sh
 
-show_links     = yes
-link_dims      = 4p,4p,8p,4p,4p
-link_thickness = 5p
-link_color     = black
+################################################
+### Function to create feature labels config ###
+################################################
+source ${SCRIPT_DIR}/../src/labels.sh
 
-label_size   = 30p
-
-padding  = 0p
-rpadding = 0p
-
-</plot>
-EOM
-
-# read gff and create TSV file
-}
+###############################################
+### Function to create feature TILES config ###
+###############################################
+source ${SCRIPT_DIR}/../src/tiles.sh
 
 ###########################################
 ### Function to create circos.conf file ###
 ###########################################
-write_circos()
-{
-cat << EOF
-# MINIMUM CIRCOS CONFIGURATION
-
-# Defines unit length for ideogram and tick spacing, referenced
-# using "u" prefix, e.g. 10u
-chromosomes_units = 500000
-
-# Show all chromosomes in karyotype file. By default, this is
-# true. If you want to explicitly specify which chromosomes
-# to draw, set this to 'no' and use the 'chromosomes' parameter.
-chromosomes_display_default = no
-${CUSTOM_CHR_LINE}
-
-# Chromosome name, size and color definition
-karyotype = circos.sequences.txt
-
-<<include etc/colors_fonts_patterns.conf>>
-<colors>
-</colors>
-
-<image>
-<<include etc/image.conf>>
-# overwrite auto_alpha_steps from default value included in etc/image.conf
-auto_alpha_steps* = 10
-</image>
-
-<ideogram>
-
-<spacing>
-# spacing between ideograms
-default = 0.005r
-</spacing>
-
-# ideogram position, thickness and fill
-radius           = 0.9r
-thickness        = 30p
-fill             = yes
-show_label	     = no
-label_font	     = default
-label_size	     = 40
-label_radius	 = 1r + 75p
-label_parallel	 = yes
-
-</ideogram>
-
-<links>
-	<link>
-		show     = yes
-		ribbon   = no
-		file     = ${INTRACHR_FILE}
-		radius   = 0.8r
-		tickness = 15
-
-	<rules>
-
-	<rule>
-	 # Do not show intra-chromossome links
-   condition  = var(intrachr)
-   show       = ${INTRACHR_SHOW}
-  </rule>
-
-	</rules>
-
-	</link>
-</links>
-
-# Add plots
-<plots>
-
-# GC Skew
-<plot>
-type        = histogram
-file        = GC_skew.txt
-r1          = 1.0r
-r0          = 0.8r
-thickness   = 2
-max         = 0.49999999999999173
-min         = -0.47826086956521324
-extend_bin  = yes
-orientation = out
-</plot>
-
-${LABEL_CONF}
-
-</plots>
-
-# debugging, I/O an dother system parameters
-<<include etc/housekeeping.conf>> # included from Circos distribution
-
-show_ticks = yes
-show_tick_labels = yes
-
-<ticks>
-
-skip_first_label = no
-skip_last_label  = no
-radius           = dims(ideogram,radius_outer)
-tick_separation  = 2p
-label_separation = 5p
-multiplier       = 1e-6
-color            = black
-thickness        = 4p
-size             = 20p
-
-# with you desired more ticks, add new tick inclusions as the one shown. See: http://circos.ca/documentation/tutorials/ticks_and_labels/labels/configuration
-<tick>
-spacing        = 1u
-show_label     = yes
-label_size     = 30p
-label_offset   = 10p
-format         = %d
-grid           = yes
-grid_color     = black
-grid_thickness = 1p
-grid_start     = 0.5r
-grid_end       = 0.999r
-</tick>
-
-<tick>
-skip_first_label = yes
-spacing        = 0.5u
-show_label     = yes
-label_size     = 30p
-label_offset   = 10p
-format         = %.2fMb
-grid           = yes
-grid_color     = black
-grid_thickness = 1p
-grid_start     = 0.5r
-grid_end       = 0.999r
-</tick>
-
-</ticks>
-
-EOF
-}
+source ${SCRIPT_DIR}/../src/write_circos.sh
 
 ###############################
 ### Function to plot circos ###
 ###############################
-plot_circos()
-{
-# get current dir
-CURRENT_DIR=$PWD
-
-# got to conf dir
-cd ${RESULTS}/conf/
-
-# draw
-circos
-
-# go back
-cd $CURRENT_DIR
-}
-
+source ${SCRIPT_DIR}/../src/plot_circos.sh
 
 ################################
 ### Get positional arguments ###
 ################################
-
 # No arguments given
 if [ $# -eq 0 ] ; then
     Help
@@ -413,8 +106,17 @@ case $ARGS in
       Help
       exit
       ;;
+    --threads)
+      if [ "$2" ]; then
+          export THREADS=$2
+          shift 2
+      else
+          echo -e '\nERROR: "--threads" requires a numeric argument\n'
+          exit
+      fi
+      ;;
     --outdir)
-      RESULTS=$2
+      export RESULTS=$2
       shift 2
       ;;
     --fofn)
@@ -425,7 +127,7 @@ case $ARGS in
           else
               echo "" >> $2 ;
           fi
-          FOFN=$2
+          export FOFN=$2
           shift 2
       else
           echo -e '\nERROR: "--fofn" requires an argument. Check your input.\n'
@@ -434,16 +136,25 @@ case $ARGS in
       ;;
     --labels)
       if [[ -f "$2" ]]; then
-          LABELS=$2
+          export LABELS=$2
           shift 2
       else
           echo -e '\nERROR: "--labels" requires an argument. Check your input.\n'
           exit
       fi
       ;;
+    --tiles)
+      if [[ -f "$2" ]]; then
+          export TILES=$2
+          shift 2
+      else
+          echo -e '\nERROR: "--tiles" requires an argument. Check your input.\n'
+          exit
+      fi
+      ;;
     --minlen)
       if [ "$2" ]; then
-          MINLEN=$2
+          export MINLEN=$2
           shift 2
       else
           echo -e '\nERROR: "--minlen" requires a numeric argument\n'
@@ -452,7 +163,7 @@ case $ARGS in
       ;;
     --minid)
       if [ "$2" ]; then
-          MINID=$2
+          export MINID=$2
           shift 2
       else
           echo -e '\nERROR: "--minid" requires a numeric argument\n'
@@ -461,7 +172,7 @@ case $ARGS in
       ;;
     --linklen)
       if [ "$2" ]; then
-          MINLINKLEN=$2
+          export MINLINKLEN=$2
           shift 2
       else
           echo -e '\nERROR: "--linklen" requires a numeric argument\n'
@@ -470,7 +181,7 @@ case $ARGS in
       ;;
     --gc_window)
       if [ "$2" ]; then
-          GCWINDOW=$2
+          export GCWINDOW=$2
           shift 2
       else
           echo -e '\nERROR: "--gc_window" requires a numeric argument\n'
@@ -479,7 +190,7 @@ case $ARGS in
       ;;
     --gc_step)
       if [ "$2" ]; then
-          GCSTEP=$2
+          export GCSTEP=$2
           shift 2
       else
           echo -e '\nERROR: "--gc_step" requires a numeric argument\n'
@@ -487,8 +198,8 @@ case $ARGS in
       fi
       ;;
     --show_intrachr)
-        INTRACHR_FILE="links_concatenated_colored.txt"
-        INTRACHR_SHOW="yes"
+        export INTRACHR_FILE="links_concatenated_colored.txt"
+        export INTRACHR_SHOW="yes"
         shift
       ;;
     *)
@@ -502,50 +213,6 @@ done
 ###################
 ### Exec script ###
 ###################
-
-## remove existing results
-rm -rf $RESULTS ;
-
-# Step 1
-echo " # Preparing inputs!"
-filter          ;
-
-# Step 2
-echo " # Writing karyotypes!"
-karyotype       ;
-
-# Step 3
-echo " # Finding links (all vs all blastn)!"
-find_links      ;
-parse_links     ;
-
-# Step 4
-echo " # Removing duplicate lines in conf files!"
-dedup           ;
-check_links     ;
-
-# Step 5
-echo " # Computing GC Skew!"
-gc_skew         ;
-
-# Step 6
-echo " # Wrinting circos conf file!"
-write_circos > ${RESULTS}/conf/circos.conf ;
-
-# Step 7
-echo " # Plotting circos!"
-plot_circos     ;
-
-cat << EOF
-
- # Bye Bye
- Now your plot is complete and must be available at: ${RESULTS}/conf/
-
- All the required files for a minimal circos plot have been produced and stored at ${RESULTS}/conf/.
- Now you can play with the ${RESULTS}/conf/circos.conf file in order to change the plot as you like.
-
- Remember to read the circos manual in order to understand the conf file.
-
- Have fun!
-
-EOF
+source ${SCRIPT_DIR}/../src/workflow.sh
+source ${SCRIPT_DIR}/../src/bye.sh
+workflow
diff --git a/recipe/src/bye.sh b/recipe/src/bye.sh
new file mode 100644
index 0000000..50abd06
--- /dev/null
+++ b/recipe/src/bye.sh
@@ -0,0 +1,13 @@
+read -r -d '' BYE << EOM
+
+ # Bye Bye
+ Now your plot is complete and must be available at: ${RESULTS}/conf/
+
+ All the required files for a minimal circos plot have been produced and stored at ${RESULTS}/conf/.
+ Now you can play with the ${RESULTS}/conf/circos.conf file in order to change the plot as you like.
+
+ Remember to read the circos manual in order to understand the conf file.
+
+ Have fun!
+
+EOM
diff --git a/recipe/src/check_links.sh b/recipe/src/check_links.sh
new file mode 100644
index 0000000..d758f9b
--- /dev/null
+++ b/recipe/src/check_links.sh
@@ -0,0 +1,13 @@
+check_links()
+{
+# get chrs with links
+## chr source
+cut -f 1 ${RESULTS}/conf/links_concatenated_colored.txt >> tmp.chrs
+## chr target
+cut -f 4 ${RESULTS}/conf/links_concatenated_colored.txt >> tmp.chrs
+
+# export LINE
+CHRS=$(cat tmp.chrs | sort -u | tr '\n' ';') ;
+rm tmp.chrs ;
+export CUSTOM_CHR_LINE="chromosomes = "${CHRS} ;
+}
diff --git a/recipe/src/dedup.sh b/recipe/src/dedup.sh
new file mode 100644
index 0000000..cc93348
--- /dev/null
+++ b/recipe/src/dedup.sh
@@ -0,0 +1,8 @@
+dedup()
+{
+for file in ${RESULTS}/conf/*.txt; do
+    sort -u ${file} > tmp.txt ;
+    cat tmp.txt   > ${file} ;
+    rm tmp.txt
+done
+}
diff --git a/recipe/src/filter.sh b/recipe/src/filter.sh
new file mode 100644
index 0000000..14348db
--- /dev/null
+++ b/recipe/src/filter.sh
@@ -0,0 +1,17 @@
+filter()
+{
+# create results dir
+mkdir -p $RESULTS
+
+# create dir for files
+mkdir -p ${RESULTS}/filtered
+
+# filter genomes
+IFS=','
+while read -r FASTA FASTA_PREFIX FASTA_COLOR ; do
+  name="$(basename $FASTA)" ;
+  $CONDA_PREFIX/bin/perl $CONDA_PREFIX/bin/removesmalls.pl $MINLEN $FASTA >> ${RESULTS}/filtered/"$name" ;
+  continue
+done<"$FOFN"
+
+}
diff --git a/recipe/src/find_links.sh b/recipe/src/find_links.sh
new file mode 100644
index 0000000..395d608
--- /dev/null
+++ b/recipe/src/find_links.sh
@@ -0,0 +1,22 @@
+find_links()
+{
+# create dir
+mkdir -p ${RESULTS}/all_vs_all_blast
+
+# concatenate genomes
+cat ${RESULTS}/filtered/* >> ${RESULTS}/all_vs_all_blast/concatenated_genomes.fasta ;
+export CONCAT_FASTA=${RESULTS}/all_vs_all_blast/concatenated_genomes.fasta
+export BLAST_DB=${RESULTS}/all_vs_all_blast/blast_db
+
+# Run blast
+makeblastdb -in $CONCAT_FASTA -dbtype nucl -out $BLAST_DB &> /dev/null ;
+blastn -task blastn -perc_identity $MINID -query $CONCAT_FASTA -db $BLAST_DB \
+    -outfmt "6 qseqid qstart qend sseqid sstart send pident length mismatch gapopen evalue bitscore stitle" \
+    -out ${RESULTS}/all_vs_all_blast/tmp.blast -num_threads $THREADS
+
+# Filter blast
+awk -F '\t' -v minid=$MINID '{ if ($7 >= minid) { print } }' ${RESULTS}/all_vs_all_blast/tmp.blast > ${RESULTS}/all_vs_all_blast/all_vs_all.blast
+
+# Remove tmp
+rm ${RESULTS}/all_vs_all_blast/tmp.blast
+}
diff --git a/recipe/src/gc_skew.sh b/recipe/src/gc_skew.sh
new file mode 100644
index 0000000..f37686b
--- /dev/null
+++ b/recipe/src/gc_skew.sh
@@ -0,0 +1,6 @@
+gc_skew()
+{
+# exec GCcalc.py
+$CONDA_PREFIX/bin/python3 $CONDA_PREFIX/bin/GCcalc.py -f ${RESULTS}/all_vs_all_blast/concatenated_genomes.fasta -w $GCWINDOW -s $GCSTEP | \
+    cut -f 1,2,3,5 | awk '{ if ($4 > 0) print $0 "\t" "color=dblue"; else print $0 "\t" "color=red"}' > ${RESULTS}/conf/GC_skew.txt
+}
diff --git a/recipe/src/help.sh b/recipe/src/help.sh
new file mode 100644
index 0000000..d8f1edc
--- /dev/null
+++ b/recipe/src/help.sh
@@ -0,0 +1,53 @@
+Help()
+{
+cat << EOF
+
+Simple script to create a circos plot between two FASTA files.
+Copyright, Felipe Almeida <almeidafmarques@outlook.com>, 2021
+
+ Syntax: plot_circos.sh [-h] [--fofn <file> --outdir <outdir> --minlen <int> --minid <int>
+                              --linklen <int> --show_intrachr --gc_window <int> --gc_step <int>
+                              --labels <file> ]
+
+ Options:
+
+ # Help
+ -h/--help                           Print this help
+
+ # Threads for blastn
+ --threads                          Number of threads to use [Default: 1]
+
+ # Output
+ --outdir                            Path to output directory [Default: ./results]
+
+ # Input file of file names
+ # CSV: fasta path,prefix,color
+ --fofn                              File of file names contatining list of fastas to
+                                     draw circos plot.
+
+ # Input min. length
+ --minlen                            Min size of contigs to consider for plot [Default: 10000]
+
+ # Links (blastn) min. percentage id
+ --minid                             Min. percentage id to filter the results of blastn to draw links [Default: 85]
+ --linklen                           Min. link (blastn hit) length to display in plot [Default: 5000]
+ --show_intrachr                     Tells the program to create a conf file showing intra chr links [Default: false]
+                                     Mandatory if using only one FASTA, otherwise, links will not be shown.
+
+ # GC skew config
+ --gc_window                         GC skew window size [Default: 5000]
+ --gc_step                           GC skew step size [Default: 5000]
+
+ # Labels config
+ --labels                            TSV file containing the label definitions for plotting. The file must contain
+                                     3 or 4 columns as shown at http://circos.ca/documentation/tutorials/2d_tracks/text_1/lesson,
+                                     "DATA FORMAT" section. The first column must be the name (ID) of the contig.
+
+ # Tiles config
+ --tiles                             TSV file containing the tile definitions for plotting. The file must contain
+                                     3 or 4 columns as shown at http://circos.ca/documentation/tutorials/configuration/data_files.
+                                     The first column must be the name (ID) of the contig.
+
+
+EOF
+}
diff --git a/recipe/src/karyotypes.sh b/recipe/src/karyotypes.sh
new file mode 100644
index 0000000..1f62d34
--- /dev/null
+++ b/recipe/src/karyotypes.sh
@@ -0,0 +1,15 @@
+karyotype()
+{
+# create dir
+mkdir -p ${RESULTS}/conf
+
+# write karyotypes
+IFS=','
+while read -r FASTA FASTA_PREFIX FASTA_COLOR ; do
+  name="$(basename $FASTA)" ;
+  FILTERED_FASTA=${RESULTS}/filtered/"$name" ;
+  bioawk -c fastx -v p=$FASTA_PREFIX -v color=$FASTA_COLOR \
+    '{ printf "chr - " substr($name,1) " " p":" substr($name,1) " " "0" " " length($seq) " " color"\n" }' \
+    $FILTERED_FASTA >> ${RESULTS}/conf/circos.sequences.txt ;
+done<"$FOFN"
+}
diff --git a/recipe/src/labels.sh b/recipe/src/labels.sh
new file mode 100644
index 0000000..5511667
--- /dev/null
+++ b/recipe/src/labels.sh
@@ -0,0 +1,28 @@
+labels()
+{
+# Create label definition
+read -r -d '' LABELS_CONF << EOM
+# Labels
+# to understand it more read: http://circos.ca/documentation/tutorials/2d_tracks/text_1/lesson
+<plot>
+label_snuggle    = yes
+type             = text
+color            = black
+file             = ${LABELS}
+
+r0 = 1r
+r1 = 1r+200p
+
+show_links     = yes
+link_dims      = 4p,4p,8p,4p,4p
+link_thickness = 5p
+link_color     = black
+
+label_size   = 30p
+
+padding  = 0p
+rpadding = 0p
+
+</plot>
+EOM
+}
diff --git a/recipe/src/parse_links.sh b/recipe/src/parse_links.sh
new file mode 100644
index 0000000..c06af46
--- /dev/null
+++ b/recipe/src/parse_links.sh
@@ -0,0 +1,21 @@
+parse_links()
+{
+# create dir
+mkdir -p ${RESULTS}/conf
+
+# Filter blocks with more then N bp hits
+awk -v minlen=$MINLINKLEN '{ if ($8 >= minlen) { print } }' \
+  ${RESULTS}/all_vs_all_blast/all_vs_all.blast | cut -f 1,2,3,4,5,6 >> ${RESULTS}/conf/links_concatenated.txt ;
+
+# get links comming from contigs and give it colors
+IFS=','
+while read -r FASTA FASTA_PREFIX FASTA_COLOR ; do
+  bioawk -c fastx '{ printf $name"\n" }' $FASTA > tmp_names.fasta ;
+  awk -v color1=$FASTA_COLOR -F'\t' 'NR==FNR{c[$1]++;next};c[$1] > 0 {print $0 "\t" "color="color1}' \
+    tmp_names.fasta ${RESULTS}/conf/links_concatenated.txt >> ${RESULTS}/conf/links_concatenated_colored.txt
+  rm tmp_names.fasta ;
+done<"$FOFN"
+
+# create additional file whithout intrachr links
+awk -F'\t' '{ if ($1 != $4) { print } }' ${RESULTS}/conf/links_concatenated_colored.txt > ${RESULTS}/conf/links_concatenated_colored_no_intrachr.txt ;
+}
diff --git a/recipe/src/plot_circos.sh b/recipe/src/plot_circos.sh
new file mode 100644
index 0000000..6282fbb
--- /dev/null
+++ b/recipe/src/plot_circos.sh
@@ -0,0 +1,14 @@
+plot_circos()
+{
+# get current dir
+CURRENT_DIR=$PWD
+
+# got to conf dir
+cd ${RESULTS}/conf/
+
+# draw
+circos
+
+# go back
+cd $CURRENT_DIR
+}
diff --git a/recipe/src/tiles.sh b/recipe/src/tiles.sh
new file mode 100644
index 0000000..7ace359
--- /dev/null
+++ b/recipe/src/tiles.sh
@@ -0,0 +1,31 @@
+tiles()
+{
+# Create label definition
+read -r -d '' TILES_CONF << EOM
+# Tiles
+# to understand its configuration read: http://circos.ca/documentation/tutorials/2d_tracks/tiles/configuration
+<plot>
+type              = tile
+layers_overflow   = grow
+file              = ${TILES}
+r1                = 0.8r
+r0                = 0.7r
+orientation       = out
+
+layers      = 5
+margin      = 0.02u
+thickness   = 15
+padding     = 8
+
+stroke_thickness = 1
+stroke_color     = grey
+
+<backgrounds>
+<background>
+color = vvlgrey
+</background>
+</backgrounds>
+
+</plot>
+EOM
+}
diff --git a/recipe/src/workflow.sh b/recipe/src/workflow.sh
new file mode 100644
index 0000000..3008806
--- /dev/null
+++ b/recipe/src/workflow.sh
@@ -0,0 +1,58 @@
+workflow()
+{
+  ## remove existing results
+  rm -rf $RESULTS ;
+
+  # Step 1
+  echo " # Preparing inputs!"
+  filter          ;
+
+  # Step 2
+  echo " # Writing karyotypes!"
+  karyotype       ;
+
+  # Step 3
+  echo " # Finding links (all vs all blastn)!"
+  find_links      ;
+  parse_links     ;
+
+  # Step 4
+  echo " # Removing duplicate lines in conf files!"
+  dedup           ;
+  check_links     ;
+
+  # Step 5
+  echo " # Computing GC Skew!"
+  gc_skew         ;
+
+  # Step 6
+  # Check for labels
+  if [ -z "$LABELS" ]
+  then
+    echo "" > /dev/null ;
+  else
+    echo " # Parsing labels!" ;
+    labels                    ;
+  fi
+
+  # Step 7
+  # Check for tiles
+  if [ -z "$TILES" ]
+  then
+    echo "" > /dev/null ;
+  else
+    echo " # Parsing tiles!" ;
+    tiles                    ;
+  fi
+
+  # Step 6
+  echo " # Wrinting circos conf file!"
+  write_circos > ${RESULTS}/conf/circos.conf ;
+
+  # Step 7
+  echo " # Plotting circos!"
+  plot_circos     ;
+
+  # Bye
+  echo ${BYE}
+}
diff --git a/recipe/src/write_circos.sh b/recipe/src/write_circos.sh
new file mode 100644
index 0000000..dc56696
--- /dev/null
+++ b/recipe/src/write_circos.sh
@@ -0,0 +1,140 @@
+write_circos()
+{
+cat << EOF
+# MINIMUM CIRCOS CONFIGURATION
+
+# Defines unit length for ideogram and tick spacing, referenced
+# using "u" prefix, e.g. 10u
+chromosomes_units = 500000
+
+# Show all chromosomes in karyotype file. By default, this is
+# true. If you want to explicitly specify which chromosomes
+# to draw, set this to 'no' and use the 'chromosomes' parameter.
+chromosomes_display_default = no
+${CUSTOM_CHR_LINE}
+
+# Chromosome name, size and color definition
+karyotype = circos.sequences.txt
+
+<<include etc/colors_fonts_patterns.conf>>
+<colors>
+</colors>
+
+<image>
+<<include etc/image.conf>>
+# overwrite auto_alpha_steps from default value included in etc/image.conf
+auto_alpha_steps* = 10
+</image>
+
+<ideogram>
+
+<spacing>
+# spacing between ideograms
+default = 0.005r
+</spacing>
+
+# ideogram position, thickness and fill
+radius           = 0.9r
+thickness        = 30p
+fill             = yes
+show_label	     = no
+label_font	     = default
+label_size	     = 40
+label_radius	   = 1r + 75p
+label_parallel	 = yes
+
+</ideogram>
+
+<links>
+	<link>
+		show     = yes
+		ribbon   = no
+		file     = ${INTRACHR_FILE}
+		radius   = 0.7r
+		tickness = 15
+
+	<rules>
+
+	<rule>
+	 # Do not show intra-chromossome links
+   condition  = var(intrachr)
+   show       = ${INTRACHR_SHOW}
+  </rule>
+
+	</rules>
+
+	</link>
+</links>
+
+# Add plots
+<plots>
+
+# GC Skew
+<plot>
+type        = histogram
+file        = GC_skew.txt
+r1          = 1.0r
+r0          = 0.8r
+thickness   = 2
+max         = 0.49999999999999173
+min         = -0.47826086956521324
+extend_bin  = yes
+orientation = out
+</plot>
+
+${LABELS_CONF}
+
+${TILES_CONF}
+
+</plots>
+
+# debugging, I/O an dother system parameters
+<<include etc/housekeeping.conf>> # included from Circos distribution
+
+show_ticks = yes
+show_tick_labels = yes
+
+<ticks>
+
+skip_first_label = no
+skip_last_label  = no
+radius           = dims(ideogram,radius_outer)
+tick_separation  = 2p
+label_separation = 5p
+multiplier       = 1e-6
+color            = black
+thickness        = 4p
+size             = 20p
+
+# with you desired more ticks, add new tick inclusions as the one shown. See: http://circos.ca/documentation/tutorials/ticks_and_labels/labels/configuration
+<tick>
+spacing        = 1u
+show_label     = yes
+label_size     = 30p
+label_offset   = 10p
+format         = %d
+grid           = yes
+grid_color     = black
+grid_thickness = 1p
+grid_start     = 0.5r
+grid_end       = 0.999r
+</tick>
+
+<tick>
+skip_first_label = yes
+spacing        = 0.5u
+show_label     = yes
+label_size     = 30p
+label_offset   = 10p
+format         = %.2fMb
+grid           = yes
+grid_color     = black
+grid_thickness = 1p
+grid_start     = 0.5r
+grid_end       = 0.999r
+</tick>
+
+</ticks>
+
+EOF
+}