release candidate 20211212

yjx1217 · Dec 25, 2021 · e2dbe6c · e2dbe6c
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diff --git a/Example_Outputs/P1-P2.simulated_tetrad.genotype.plot.pdf b/Example_Outputs/P1-P2.simulated_tetrad.genotype.plot.pdf
diff --git a/Example_Outputs/P1-P2.simulated_tetrad.genotype.txt.gz b/Example_Outputs/P1-P2.simulated_tetrad.genotype.txt.gz
diff --git a/Example_Outputs/P1-P2.simulated_tetrad.linkage_blocks.txt.gz b/Example_Outputs/P1-P2.simulated_tetrad.linkage_blocks.txt.gz
diff --git a/Example_Outputs/P1-P2.simulated_tetrad.recombination_events.txt.gz b/Example_Outputs/P1-P2.simulated_tetrad.recombination_events.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.detailed.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.detailed.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.genotype_plot.pdf b/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.genotype_plot.pdf
diff --git a/....AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.co_associated_gc.txt.gz b/....AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.co_associated_gc.txt.gz
diff --git a/....AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.event_type_count.txt.gz b/....AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.event_type_count.txt.gz
diff --git a/.../S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.events.txt.gz b/.../S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.events.txt.gz
diff --git a/...K1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.linkage_blocks.txt.gz b/...K1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.linkage_blocks.txt.gz
diff --git a/...S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.markers.txt.gz b/...S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.markers.txt.gz
diff --git a/...C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.merging_log.txt.gz b/...C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.recombination_profile.merging_log.txt.gz
diff --git a/....S288C.q50.genotype.lite.inferred.recombination_profile.preliminary_linkage_blocks.txt.gz b/....S288C.q50.genotype.lite.inferred.recombination_profile.preliminary_linkage_blocks.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.inferred.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.genotype_plot.pdf b/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.genotype_plot.pdf
diff --git a/...C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.co_associated_gc.txt.gz b/...C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.co_associated_gc.txt.gz
diff --git a/...C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.event_type_count.txt.gz b/...C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.event_type_count.txt.gz
diff --git a/...tputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.events.txt.gz b/...tputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.events.txt.gz
diff --git a/...88C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.linkage_blocks.txt.gz b/...88C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.linkage_blocks.txt.gz
diff --git a/...puts/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.markers.txt.gz b/...puts/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.markers.txt.gz
diff --git a/.../S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.merging_log.txt.gz b/.../S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.recombination_profile.merging_log.txt.gz
diff --git a/...702-8.S288C.q50.genotype.lite.raw.recombination_profile.preliminary_linkage_blocks.txt.gz b/...702-8.S288C.q50.genotype.lite.raw.recombination_profile.preliminary_linkage_blocks.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.S288C.q50.genotype.lite.raw.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.detailed.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.detailed.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.genotype_plot.pdf b/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.genotype_plot.pdf
diff --git a/...K1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.co_associated_gc.txt.gz b/...K1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.co_associated_gc.txt.gz
diff --git a/...K1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.event_type_count.txt.gz b/...K1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.event_type_count.txt.gz
diff --git a/...ts/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.events.txt.gz b/...ts/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.events.txt.gz
diff --git a/...-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.linkage_blocks.txt.gz b/...-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.linkage_blocks.txt.gz
diff --git a/...s/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.markers.txt.gz b/...s/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.markers.txt.gz
diff --git a/...88C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.merging_log.txt.gz b/...88C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.recombination_profile.merging_log.txt.gz
diff --git a/...-8.SK1.q50.genotype.lite.inferred.recombination_profile.preliminary_linkage_blocks.txt.gz b/...-8.SK1.q50.genotype.lite.inferred.recombination_profile.preliminary_linkage_blocks.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.inferred.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.genotype_plot.pdf b/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.genotype_plot.pdf
diff --git a/...88C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.co_associated_gc.txt.gz b/...88C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.co_associated_gc.txt.gz
diff --git a/...88C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.event_type_count.txt.gz b/...88C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.event_type_count.txt.gz
diff --git a/...Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.events.txt.gz b/...Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.events.txt.gz
diff --git a/...S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.linkage_blocks.txt.gz b/...S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.linkage_blocks.txt.gz
diff --git a/...utputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.markers.txt.gz b/...utputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.markers.txt.gz
diff --git a/...ts/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.merging_log.txt.gz b/...ts/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.recombination_profile.merging_log.txt.gz
diff --git a/...D1702-8.SK1.q50.genotype.lite.raw.recombination_profile.preliminary_linkage_blocks.txt.gz b/...D1702-8.SK1.q50.genotype.lite.raw.recombination_profile.preliminary_linkage_blocks.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.SK1.q50.genotype.lite.raw.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.detailed.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.detailed.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.genotype_plot.pdf b/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.genotype_plot.pdf
diff --git a/...K1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.co_associated_gc.txt.gz b/...K1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.co_associated_gc.txt.gz
diff --git a/...K1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.event_type_count.txt.gz b/...K1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.event_type_count.txt.gz
diff --git a/...ts/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.events.txt.gz b/...ts/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.events.txt.gz
diff --git a/...-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.linkage_blocks.txt.gz b/...-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.linkage_blocks.txt.gz
diff --git a/...s/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.markers.txt.gz b/...s/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.markers.txt.gz
diff --git a/...88C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.merging_log.txt.gz b/...88C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.recombination_profile.merging_log.txt.gz
diff --git a/...-8.ref.q50.genotype.lite.inferred.recombination_profile.preliminary_linkage_blocks.txt.gz b/...-8.ref.q50.genotype.lite.inferred.recombination_profile.preliminary_linkage_blocks.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.inferred.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.genotype_plot.pdf b/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.genotype_plot.pdf
diff --git a/...88C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.co_associated_gc.txt.gz b/...88C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.co_associated_gc.txt.gz
diff --git a/...88C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.event_type_count.txt.gz b/...88C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.event_type_count.txt.gz
diff --git a/...Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.events.txt.gz b/...Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.events.txt.gz
diff --git a/...S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.linkage_blocks.txt.gz b/...S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.linkage_blocks.txt.gz
diff --git a/...utputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.markers.txt.gz b/...utputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.markers.txt.gz
diff --git a/...ts/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.merging_log.txt.gz b/...ts/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.recombination_profile.merging_log.txt.gz
diff --git a/...D1702-8.ref.q50.genotype.lite.raw.recombination_profile.preliminary_linkage_blocks.txt.gz b/...D1702-8.ref.q50.genotype.lite.raw.recombination_profile.preliminary_linkage_blocks.txt.gz
diff --git a/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.txt.gz b/Example_Outputs/S288C-SK1.AND1702-8.ref.q50.genotype.lite.raw.txt.gz
diff --git a/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.intermarker_distance.txt.gz b/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.intermarker_distance.txt.gz
diff --git a/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.pdf b/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.pdf
diff --git a/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.txt.gz b/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.txt.gz
diff --git a/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.vcf.gz b/Example_Outputs/S288C-SK1.S288C.final.SNP.markers.vcf.gz
diff --git a/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.intermarker_distance.txt.gz b/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.intermarker_distance.txt.gz
diff --git a/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.pdf b/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.pdf
diff --git a/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.txt.gz b/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.txt.gz
diff --git a/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.vcf.gz b/Example_Outputs/S288C-SK1.SK1.final.SNP.markers.vcf.gz
diff --git a/Example_Outputs/S288C-SK1.ref.final.SNP.markers.intermarker_distance.txt.gz b/Example_Outputs/S288C-SK1.ref.final.SNP.markers.intermarker_distance.txt.gz
diff --git a/Example_Outputs/S288C-SK1.ref.final.SNP.markers.pdf b/Example_Outputs/S288C-SK1.ref.final.SNP.markers.pdf
diff --git a/Example_Outputs/S288C-SK1.ref.final.SNP.markers.txt.gz b/Example_Outputs/S288C-SK1.ref.final.SNP.markers.txt.gz
diff --git a/Manual.docx b/Manual.docx
diff --git a/Manual.pdf b/Manual.pdf
diff --git a/...e/Master_Sample_Table.Batch_S288C-SK1.txt → ...e/Master_Sample_Table.Batch_S288C-SK1.txt b/...e/Master_Sample_Table.Batch_S288C-SK1.txt → ...e/Master_Sample_Table.Batch_S288C-SK1.txt
diff --git a/....Tetrad_Genotyping_by_Reference_Genome.sh → ....Gamete_Genotyping_by_Reference_Genome.sh b/....Tetrad_Genotyping_by_Reference_Genome.sh → ....Gamete_Genotyping_by_Reference_Genome.sh
@@ -9,7 +9,7 @@ source ./../../env.sh
 # set project-specific variables
 batch_id="Batch_S288C-SK1" # The batch id used for the gamete read mapping analysis. Default = "Batch_S288C-SK1" 
 master_sample_table="Master_Sample_Table.${batch_id}.txt" # The master sample table for this batch. Default = "Master_Sample_Table.${batch_id}.txt".
-net_quality_cutoff=20 # The net quality cutoff for genotyping. Default = "20".
+net_quality_cutoff=50 # The net quality cutoff for genotyping. Default = "50".
 apply_cnv_filter="yes" # Whether to set gamete genotype to NA for potential CNV regions in gametes. Set this option to "no" if the gamete sequencing depth is very low (e.g. <= 1). Default = "yes".
 allow_heteroduplex="no" # Whether to consider the possibility of heteroduplex formation. Default = "no".
 chr_list="$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.chr_list.txt" # The included chromosome list for the analyzed genome. Default = "$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.chr_list.txt".

diff --git a/...rofiling_by_Reference_Genome/RecombineX.05.Recombination_Profiling_by_Reference_Genome.sh b/...rofiling_by_Reference_Genome/RecombineX.05.Recombination_Profiling_by_Reference_Genome.sh
@@ -10,29 +10,25 @@ source ./../../env.sh
 batch_id="Batch_S288C-SK1" # The batch id used for the gamete read mapping analysis. Default = "Batch_S288C-SK1".
 master_sample_table="Master_Sample_Table.$batch_id.txt" # The master sample table for this batch. Default = "Master_Sample_Table.${batch_id}.txt".
 merging_range=5000 # The distance range (bp) for merging nearby COs. Default = "5000" (i.e. 5000 bp). 
-net_quality_cutoff=20 # The net quality difference cutoff used in tetrad genotyping. Default = "20".
+net_quality_cutoff=50 # The net quality difference cutoff used in tetrad genotyping. Default = "50".
 color_scheme="$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.color_scheme.txt" # The color scheme to use for plotting genotypes. Default = "$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.color_scheme.txt".
-plot_individual_recombination_event="yes" # Whether to plot individual recombination event, "yes" by default. Default = "yes".
+plot_individual_recombination_event="no" # Whether to plot individual recombination event: "yes" or "no". Default = "no".
 flanking="4000" # The recombination event flanking region (bp) for plotting. Default = "4000".
 debug="no" # Whether to keep intermediate files for debuging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 ###########################################
 
 
-
-
-
 # process the pipeline
 ###########################################
 # Normally no need to change the following parameters
 genome_dir="./../01.Reference_Genome_Preprocessing" # The relative path to the 01.Reference_Genome_Preprocessing.
-genotype_dir="./../04.Tetrad_Genotyping_by_Reference_Genome" # The relative path to the 04.Tetrad_Genotyping_by_Reference_Genome directory.
+genotype_dir="./../04.Gamete_Genotyping_by_Reference_Genome" # The relative path to the 04.Gamete_Genotyping_by_Reference_Genome directory.
 output_dir=$batch_id # output directory to create within this current directory
 min_marker_number=1 # The minimal number of markers to be considered for trustful linkage blocks. Default = "1".
 min_block_size=1 # The minimal marker-bounded block size (bp) to be considered for trustful linkage blocks. Default = "1" (i.e. 1 bp).
 ###########################################
 
 
-
 # filtering tetrads by spore mapping depth
 #perl $RECOMBINEX_HOME/scripts/filter_tetrads_by_sequencing_depth.pl  -i $master_sample_table -o $master_sample_table.filtered \
 #    -d $spore_mapping_depth -c $mapping_depth_cutoff  

diff --git a/...s/Master_Sample_Table.Batch_S288C-SK1.txt → ...s/Master_Sample_Table.Batch_S288C-SK1.txt b/...s/Master_Sample_Table.Batch_S288C-SK1.txt → ...s/Master_Sample_Table.Batch_S288C-SK1.txt
diff --git a/...16.Tetrad_Genotyping_by_Parent_Genomes.sh → ...16.Gamete_Genotyping_by_Parent_Genomes.sh b/...16.Tetrad_Genotyping_by_Parent_Genomes.sh → ...16.Gamete_Genotyping_by_Parent_Genomes.sh
@@ -10,7 +10,7 @@ source ./../../env.sh
 batch_id="Batch_S288C-SK1" # The batch id used for gamete read mapping. Default = "Batch_S288C-SK1". 
 master_sample_table="Master_Sample_Table.${batch_id}.txt" # The master sample table for this batch. Default = "Master_Sample_Table.${batch_id}.txt".
 marker_dir="./../14.Polymorphic_Markers_by_Consensus" # The relative path to the "12.Polymorphic_Markers_by_Cross_Parent_Genome_Alignment" or "14.Polymorphic_Markers_by_Consensus" directory (for parental-genome-based analysis). Default = ./../14.Polymorphic_Markers_by_Consensus".
-net_quality_cutoff=20 # The net quality cutoff for genotyping. Default = "20".
+net_quality_cutoff=50 # The net quality cutoff for genotyping. Default = "50".
 apply_cnv_filter="yes" # Whether to set gamete genotype to NA for potential CNV regions in gametes. Set this option to "no" if the gamete sequencing depth is very low (e.g. <= 1). Default = "yes".
 allow_heteroduplex="no" # Whether to consider the possibility of heteroduplex formation. Default = "no". 
 chr_list="$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.chr_list.txt" # The chromosome list for the analyzed genome. Default = "$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.chr_list.txt".

diff --git a/...on_Profiling_by_Parent_Genomes/RecombineX.17.Recombination_Profiling_by_Parent_Genomes.sh b/...on_Profiling_by_Parent_Genomes/RecombineX.17.Recombination_Profiling_by_Parent_Genomes.sh
@@ -10,9 +10,9 @@ source ./../../env.sh
 batch_id="Batch_S288C-SK1" # The batch id used for the gamete read mapping analysis. Default = "Batch_S288C-SK1".
 master_sample_table="Master_Sample_Table.$batch_id.txt" # The master sample table for this batch. Default = "Master_Sample_Table.${batch_id}.txt".
 merging_range=5000 # The distance range (bp) for merging nearby COs. Default = "5000" (i.e. 5000 bp). 
-net_quality_cutoff=20 # The net quality difference cutoff used in tetrad genotyping. Default = "20".
+net_quality_cutoff=50 # The net quality difference cutoff used in tetrad genotyping. Default = "50".
 color_scheme="$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.color_scheme.txt" # The color scheme to use for plotting genotypes. Default = "$RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.color_scheme.txt".
-plot_individual_recombination_event="yes" # Whether to plot individual recombination event, "yes" by default. Default = "yes".
+plot_individual_recombination_event="no" # Whether to plot individual recombination event: "yes" or "no". Default = "no".
 flanking="4000" # The recombination event flanking region (bp) for plotting. Default = "4000".
 debug="no" # Whether to keep intermediate files for debuging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 ###########################################
@@ -21,7 +21,7 @@ debug="no" # Whether to keep intermediate files for debuging. Use "yes" if prefe
 ###########################################
 # Normally no need to change the following parameters
 genome_dir="./../11.Parent_Genome_Preprocessing" # The relative path to the 11.Parent_Genome_Preprocessing directory.
-genotype_dir="./../16.Tetrad_Genotyping_by_Parent_Genomes" # The relative path to the 16.Tetrad_Genotyping_by_Parent_Genomes directory.
+genotype_dir="./../16.Gamete_Genotyping_by_Parent_Genomes" # The relative path to the 16.Gamete_Genotyping_by_Parent_Genomes directory.
 output_dir=$batch_id # output directory to create within this current directory
 min_marker_number=1 # The minimal number of markers to be considered for trustful linkage blocks. Default = "1".
 min_block_size=1 # The minimal marker-bounded block size (bp) to be considered for trustful linkage blocks. Default = "1" (i.e. 1 bp).

diff --git a/README.md b/README.md
@@ -1,20 +1,20 @@
 # RecombineX
 
 <p align="center">
-  <img src="https://github.com/yjx1217/RecombineX/blob/master/RecombineX.logo.png" alt="RecombineX logo" width="547" height="162"/>
+  <img src="https://github.com/yjx1217/RecombineX/blob/master/RecombineX.logo.png" alt="RecombineX_logo" width="547" height="162"/>
 </p>
 
-**RecombineX: a computational framework for tetrad-based meiotic recombination analysis**
+**RecombineX: a computational framework for high-throughput gamete genotyping and tetrad-based meiotic recombination analysis**
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 ## Description
 <div style="text-align: justify"> 
-RecombineX is a computational framework for tetrad-based genotyping and meiotic recombination analysis. It handles the full workflow of marker identification, tetrad genotyping, as well as recombination events profiling and classification and produces publication-quality plots. In addition to the conventional reference-genome-based approach, RecombineX also supports the analysis based on the native parent genomes, therefore permitting the close examination on how native parent genomic backgrounds may affect meiotic recombination landscapes of the resulting tetrads. Moreover, RecombineX can also handle partially viable tetrads (e.g. the tetrad with only 3 viable gametes) with its genotype inference feature, which is very useful for studying genome incompatibility. Also, RecombineX shines in its high scalability, capable of processing thousands of sequenced tetrads. Finally, we also developed a tetrad simulation module for RecombineX, which provides rich parameters for users to simulate recombinant tetrads with all introduced recombination events recorded in detail, which can be very useful for downstream hypothesis testing and software development.
+Meiotic recombination is an essential biological process that ensures faithful chromosome segregation and promotes parental allele reshuffling. Tetrad analysis is a powerful approach to quantify the genetic makeups and recombination landscapes of meiotic products. Here we present RecombineX, an integrated computational framework that automates the full workflow of marker identification, gamete genotyping, and tetrad-based recombination profiling in a high-throughput fashion, capable of processing hundreds of tetrads in a single batch. Aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which enables analyzing meiotic recombination landscapes in their native genomic contexts. Additional features such as copy number variation profiling and missing genotype inference further enhance downstream analysis. RecombineX also includes a dedicate module for simulating the genomes and reads of recombinant tetrads for any given organisms, which enables fine-tuned simulation-based hypothesis testing. 
 </div>
 
 <p align="center">
-  <img src="https://github.com/yjx1217/RecombineX/blob/master/RecombineX.overview.png" alt="RecombineX logo" width="915" height="888"/>
+  <img src="https://github.com/yjx1217/RecombineX/blob/master/RecombineX.overview.png" alt="RecombineX_overview" width="915" height="888"/>
 </p>
 
 Under the hood, a series of task-specific modules are provided to carry out the full workflow of RecombineX:
@@ -33,8 +33,8 @@ Under the hood, a series of task-specific modules are provided to carry out the
   * identifying polymorphic markers between the two crossing parents based on the reference genome (for the "reference-based" mode only)
 * **03.Gamete_Read_Mapping_to_Reference_Genome**
   * mapping the reads of labeled gametes to the reference genome (for the "reference-based" mode only)
-* **04.Tetrad_Genotyping_by_Reference_Genome**
-  * assigning genotypes to labeled gametes from the same tetrad based on the reference genome (for the "reference-based" mode only)
+* **04.Gamete_Genotyping_by_Reference_Genome**
+  * assigning genotypes to a list of pre-defined gametes based on the reference genome (for the "reference-based" mode only)
 * **05.Recombination_Profiling_by_Reference_Genome**
   * profiling and classifying recombination events for each tetrad based on the reference genome (for the "reference-based" mode only)
 * **11.Parent_Genome_Preprocessing**
@@ -47,8 +47,8 @@ Under the hood, a series of task-specific modules are provided to carry out the
   * identifying consensus polymorphic markers between the two crossing parents based on both whole genome alignment and cross-parent read mapping (for the "parent-based" mode only)
 * **15.Gamete_Read_Mapping_to_Parent_Genomes**
   * mapping the reads of labeled gametes to the genomes of two native parents (for the "parent-based" mode only)
-* **16.Tetrad_Genotyping_by_Parent_Genomes**
-  * assigning genotypes to labeled gametes from the same tetrad based on parent genomes (for the "parent-based" mode only)
+* **16.Gamete_Genotyping_by_Parent_Genomes**
+  * assigning genotypes to a list of pre-defined gametes from the same tetrad based on parent genomes (for the "parent-based" mode only)
 * **17.Recombination_Profiling_by_Parent_Genomes**
   * profiling and classifying recombination events for each tetrad based on parent genomes (for the "parent-based" mode only)
 * **20.Recombinant_Tetrad_Simulation**

diff --git a/RecombineX.overview.png b/RecombineX.overview.png
diff --git a/data/AND1702_12a.assembly.final.fa.gz b/data/AND1702_12a.assembly.final.fa.gz
diff --git a/data/AND1702_12a.assembly.final.gff3.gz b/data/AND1702_12a.assembly.final.gff3.gz
diff --git a/data/AND1702_8a.assembly.final.fa.gz b/data/AND1702_8a.assembly.final.fa.gz
diff --git a/data/AND1702_8a.assembly.final.gff3.gz b/data/AND1702_8a.assembly.final.gff3.gz
diff --git a/data/Chlamydomonas_reinhardtii.color_scheme.txt b/data/Chlamydomonas_reinhardtii.color_scheme.txt
@@ -1,6 +1,5 @@
 NA	#e5e5e5
 CC408	#ffff33
-CC2935	#0099ff
 CC2936	#4daf4a
-CC1010	#ff3300
-CC124	#4daf4a
+heteroduplex	#ffc425
+
diff --git a/data/Saccharomyces_cerevisiae.color_scheme.txt b/data/Saccharomyces_cerevisiae.color_scheme.txt
@@ -1,10 +1,11 @@
-NA	#e5e5e5
-P1	#ff3300
-P2	#0099ff
-S288C	#ff3300
-SK1	#0099ff
-DBVPG6044	#ff3300
-DBVPG6765	#66cc33
-Y12	#0099ff
-YPS128	#ffcc00
-heteroduplex	#ffc425
+NA	"#e5e5e5"
+heteroduplex	"#ffa500"
+#P1	"#ff3300"
+#P2	"#0099ff"
+S288C	"#ff3300"
+SK1	"#0099ff"
+#DBVPG6044	"#ff3300"
+#DBVPG6765	"#66cc33"
+#Y12	"#0099ff"
+#YPS128	"#ffcc00"
+
diff --git a/install_dependencies.sh b/install_dependencies.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# last update: 2021/03/04
+# last update: 2021/12/07
 
 set -e -o pipefail
 
@@ -148,7 +148,7 @@ VCFLIB_DOWNLOAD_URL="https://github.com/vcflib/vcflib/releases/download/v${VCFLI
 
 VT_VERSION="" # 
 VT_GITHUB_COMMIT_VERSION="f6d2b5d" # committed on 2018.08.01
-VT_DOWNLOAD_URL="https://github.com/atks/vt"
+VT_DOWNLOAD_URL="git://github.com/atks/vt"
 
 FREEC_VERSION="11.4" # released on 2018.04.27
 FREEC_DOWNLOAD_URL="https://github.com/BoevaLab/FREEC/archive/v${FREEC_VERSION}.tar.gz"
@@ -510,6 +510,7 @@ if [ -z $(check_installed $freebayes_dir) ]; then
     chmod 755 freebayes-${FREEBAYES_VERSION}-linux-static-AMD64
     ln -s freebayes-${FREEBAYES_VERSION}-linux-static-AMD64 freebayes
     cd $build_dir
+    rm freebayes-${FREEBAYES_VERSION}-src.tar.gz
     note_installed $freebayes_dir
 fi
 

diff --git a/pipelines/RecombineX.00.Prepare_Reference_Genome_for_Chlamydomonas_reinhardtii.sh b/pipelines/RecombineX.00.Prepare_Reference_Genome_for_Chlamydomonas_reinhardtii.sh
@@ -0,0 +1,65 @@
+#!/bin/bash
+set -e -o pipefail
+
+#######################################
+# load environment variables for Varathon
+source ./../../env.sh
+
+#######################################
+# set project-specific variables
+ref_genome_prefix="Chlamydomonas_reinhardtii" # The file name prefix of the reference genome. Default = "Chlamydomonas_reinhardtii". 
+ref_genome_download_URL="ftp://ftp.ensemblgenomes.org/pub/plants/release-49/fasta/chlamydomonas_reinhardtii/dna/Chlamydomonas_reinhardtii.Chlamydomonas_reinhardtii_v5.5.dna_sm.toplevel.fa.gz" # The URL for downloading the reference genome. Default = "ftp://ftp.ensemblgenomes.org/pub/plants/release-49/fasta/chlamydomonas_reinhardtii/dna/Chlamydomonas_reinhardtii.Chlamydomonas_reinhardtii_v5.5.dna_sm.toplevel.fa.gz".
+chr_list="./../../data/Chlamydomonas_reinhardtii.chr_list.txt" # The single-column list defining chromosomes/scaffolds/contigs to be included. Default = ./../../data/Chlamydomonas_reinhardtii.chr_list.txt".
+debug="no" # Whether to keep intermediate files for debuging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
+#######################################
+
+
+
+
+#######################################
+# process the pipeline
+
+download_and_extract() {
+    url=$1
+    echo "Downloading $url"
+    if [[ $url =~ \.gz$ ]]; 
+    #if [[ $url =~ \.fa.gz$ || $url =~ \.fasta.gz$ ]]; 
+    then
+	download_location="$ref_genome_prefix.raw.fa.gz"
+        extract_command="gunzip"
+	wget -c --no-check-certificate $url -O $download_location
+	gunzip $download_location
+    else
+	download_location="$ref_genome_prefix.raw.fa"
+	wget -c --no-check-certificate $url -O $download_location
+    fi
+}
+
+echo ""
+echo "Retrieve the sample reference genome assembly ..."
+download_and_extract $ref_genome_download_URL 
+echo ""
+echo "Tidy the sample reference genome assembly ..."
+$RECOMBINEX_HOME/scripts/tidy_fasta.pl -i $ref_genome_prefix.raw.fa -o $ref_genome_prefix.tidy.fa
+sed -i "s/>/>chr/gi" $ref_genome_prefix.tidy.fa
+$RECOMBINEX_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_prefix.tidy.fa -l $chr_list -m normal -o $ref_genome_prefix.tidy.lite.fa.gz
+
+if [[ $debug = "no" ]]
+then
+    echo ""
+    echo "Removing intermediate files ..."
+    rm $ref_genome_prefix.raw.fa
+    rm $ref_genome_prefix.tidy.fa
+fi
+
+############################
+# checking bash exit status
+if [[ $? -eq 0 ]]
+then
+    echo ""
+    echo "RecombineX message: This bash script has been successfully processed! :)"
+    echo ""
+    echo ""
+    exit 0
+fi
+############################
diff --git a/pipelines/RecombineX.00.Prepare_Reference_Genome_for_Saccharomyces_cerevisiae.sh b/pipelines/RecombineX.00.Prepare_Reference_Genome_for_Saccharomyces_cerevisiae.sh
@@ -0,0 +1,53 @@
+#!/bin/bash
+set -e -o pipefail
+
+#######################################
+# load environment variables for RecombineX
+source ./../../env.sh
+
+#######################################
+# set project-specific variables
+
+debug="no" # Whether to keep intermediate files for debuging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
+
+#######################################
+
+
+
+######################################
+# process the pipeline
+echo "retrieve sample reference genome data ..."
+wget -c https://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz
+tar -xvzf S288C_reference_genome_R64-2-1_20150113.tgz
+cp ./S288C_reference_genome_R64-2-1_20150113/S288C_reference_sequence_R64-2-1_20150113.fsa  SGDref.genome.raw.fa
+cp ./S288C_reference_genome_R64-2-1_20150113/saccharomyces_cerevisiae_R64-2-1_20150113.gff SGDref.all_feature.gff
+perl $RECOMBINEX_HOME/scripts/tidy_SGDref_genome.pl -i SGDref.genome.raw.fa -o SGDref.genome.tidy.fa
+perl $RECOMBINEX_HOME/scripts/select_fasta_by_list.pl -i SGDref.genome.tidy.fa -l $RECOMBINEX_HOME/data/Saccharomyces_cerevisiae.chr_list.txt -o SGDref.genome.fa -m normal
+gzip SGDref.genome.fa
+perl $RECOMBINEX_HOME/scripts/filter_gff_by_feature.pl -i SGDref.all_feature.gff -o SGDref.centromere.gff -f centromere -m keep
+
+# echo "retrieve sample subtelomere GFF files ..."
+# cp $RECOMBINEX_HOME/data/Saccharomyces_cerevisiae_subtelomere_gff3/SGDref.subtelomere.gff .
+
+if [[ $debug = "no" ]]
+then
+    echo ""
+    echo "removing intermediate files and directories ..."
+
+    rm -rf S288C_reference_genome_R64-2-1_20150113*
+    rm SGDref.genome.raw.fa
+    rm SGDref.genome.tidy.fa
+    rm SGDref.all_feature.gff
+fi
+
+############################
+# checking bash exit status
+if [[ $? -eq 0 ]]
+then
+    echo ""
+    echo "RecombineX message: This bash script has been successfully processed! :)"
+    echo ""
+    echo ""
+    exit 0
+fi
+############################
diff --git a/pipelines/RecombineX.00.Prepare_Sample_Parent_Genomes.sh b/pipelines/RecombineX.00.Prepare_Sample_Parent_Genomes.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+set -e -o pipefail
+
+#######################################
+# load environment variables for RecombineX
+source ./../../env.sh
+
+#######################################
+# set project-specific variables
+
+# none
+
+#######################################
+# process the pipeline
+
+echo "retrieve sample parental genome data ..."
+for i in S288C SK1
+do
+    cp $RECOMBINEX_HOME/data/$i.genome.fa .
+    cp $RECOMBINEX_HOME/data/$i.all_feature.gff .
+    perl $RECOMBINEX_HOME/scripts/filter_gff_by_feature.pl -i $i.all_feature.gff -o $i.centromere.gff -f centromere -m keep
+done
+
+# echo "retrieve sample subtelomere GFF files ..."
+# for i in S288C SK1
+# do
+#     cp $RECOMBINEX_HOME/data/Saccharomyces_cerevisiae_subtelomere_gff3/$i.subtelomere.gff .
+# done
+
+echo ""
+echo "removing intermediate files and directories ..."
+for i in S288C SK1
+do
+    rm $i.all_feature.gff
+done
+
+
+############################
+# checking bash exit status
+if [[ $? -eq 0 ]]
+then
+    echo ""
+    echo "RecombineX message: This bash script has been successfully processed! :)"
+    echo ""
+    echo ""
+    exit 0
+fi
+############################