Synolog: synolog

Program Options

Although most of the arguments are shared between the different options, no two options share the exact same set of flags

Options for genome

--path – path to directory containing the results generated from synolog [required]
--orgs – the names of the orgs of interest [requires >= 2 || org_list.tsv]
--out – name of the output figure [default: automatic]
--format – output format type (pdf, png, svg) [default = pdf]
--color – color the synteny lines by either chromosome [0] or synteny blocks [1] (choices: 0, 1) [default: 0]
--min – minimum length to include a chromosome [default: 1 Mb]
--no-chr-labels – if set, no chromosomal labels will be added to the image
--span – if set, only draw syntenic orthologs that span across all orgs

Options for region

--path – path to directory containing the results generated from synolog [required]
--orgs – the names of the orgs of interest [requires >= 2 || org_list.tsv]
--out – name of the output figure [default: automatic]
--region – A Chr or Chr:Start-End coordinate found in the first org in --orgs
--pixels – Number of pixels per genome section [default 150]
--format – output format type (pdf, png, svg) [default = pdf]
--all – show all elements within the region regardless of synteny information
--scale-free – draw elements without scaling for genomic distance
--no-chr-labels – if set, no chromosomal labels will be added to the image
--no-gene-labels – if set, no gene labels will be added to the image

Options for synteny

--path – path to directory containing the results generated from synolog [required]
--orgs – the names of the orgs of interest [requires >= 2 || org_list.tsv]
--out – name of the output figure [default: automatic]
--id – synteny/segmental block id between the first two org IDs in --orgs
--pixels – Number of pixels per genome section [default 150]
--format – output format type (pdf, png, svg) [default = pdf]
--color – color the synteny lines by either chromosome [0] or synteny blocks [1] (choices: 0, 1) [default: 0]
--all – show all elements within the region regardless of synteny information
--scale-free – draw elements without scaling for genomic distance
--no-chr-labels – if set, no chromosomal labels will be added to the image
--no-gene-labels – if set, no gene labels will be added to the image

Options for segmental

--path – path to directory containing the results generated from synolog [required]
--orgs – the names of the orgs of interest [requires >= 2 || org_list.tsv]
--out – name of the output figure [default: automatic]
--id – synteny/segmental block id between the first two org IDs in --orgs
--pixels – Number of pixels per genome section [default 150]
--format – output format type (pdf, png, svg) [default = pdf]
--all – show all elements within the region regardless of synteny information
--scale-free – draw elements without scaling for genomic distance
--no-chr-labels – if set, no chromosomal labels will be added to the image
--no-gene-labels – if set, no gene labels will be added to the image
--only-duplicates – if set, only the segmental duplicated genes will be drawn

Options for tree_cluster

--path – path to directory containing the results generated from synolog [required]
--orgs – the names of the orgs of interest [requires >= 2 || org_list.tsv]
--out – name of the output figure [default: automatic]
--id – tree cluster id
--pixels – Number of pixels per genome section [default 150]
--format – output format type (pdf, png, svg) [default = pdf]
--all – show all elements within the region regardless of synteny information
--scale-free – draw elements without scaling for genomic distance
--no-chr-labels – if set, no chromosomal labels will be added to the image
--no-gene-labels – if set, no gene labels will be added to the image

Example Usage

Below are some general examples for each of the different types of figures

genome-wide synteny using all orgs from an analysis % synolog_plot.py genome --path ./path/to/synolog/output_files/ \ --orgs ./path/to/orgs.tsv \ --out genome_plot.pdf \

# genome-wide synteny using a subset of orgs % synolog_plot.py genome --path ./path/to/synolog/output_files/ \ --orgs orgA,orgB,orgC \ --out genome_plot.pdf \

# region-wide synteny of a specific chromosome % synolog_plot.py region --path ./path/to/synolog/output_files/ \ --orgs ./path/to/orgs.tsv \ --region chr1 \ --out region_plot.pdf \ --no-gene-labels # prevent thousands of labels to be drawn

# region-wide synteny of a specific locus % synolog_plot.py region --path ./path/to/synolog/output_files/ \ --orgs ./path/to/orgs.tsv \ --region "chr1:start_bp-end_bp" \ --out region_plot.pdf \

# plot a specific synteny block and include all elements in the vicinity % synolog_plot.py segmental --path ./path/to/synolog/output_files/ \ --orgs ./path/to/orgs.tsv \ --id N \ # synteny block ID b/t first two orgs --all \ --no-gene-labels # prevent thousands of labels to be written --out synteny_plot.pdf

# plot a specific segmental duplication block and include all elements in the vicinity % synolog_plot.py tree_cluster --path ./path/to/synolog/output_files/ \ --orgs ./path/to/orgs.tsv \ --id N \ # segmental duplication ID --all \ --no-gene-labels # prevent thousands of labels to be written --out segmental_plot.pdf

# plot a specific tree cluster and include all elements in the vicinity % synolog_plot.py synteny --path ./path/to/synolog/output_files/ \ --orgs ./path/to/orgs.tsv \ --id N \ # tree cluster ID --all \ --no-gene-labels # prevent thousands of labels to be written --out tree_cluster_plot.pdf

The examples that follow illustrate some of the Synolog results generated using emperical data from the Manuscript

# genome-wide synteny across turtles using chromosomes >=10 Mb % synolog_plot.py genome --path ./turtle_synolog_analysis/ \ --orgs ./turtle_synolog_analysis/orgs.tsv \ --min 10e6 \ --out genome_plot.pdf

CD207 locus in turtles % synolog_plot.py region --path ./turtle_synolog_analysis/ \ --orgs ./turtle_synolog_analysis/orgs.tsv \ --region "NC_066619.1:284988000-287024000" \ --all \ --out cd207_plot.pdf

synolog_plot.py

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