About
Our project is based on perl and python written in two types of scripts, which is convenient for users to run in different environments.
Perl
In this version, we provide more comprehensive annotation information, including transition, transversion, TEs, centromeres, telomeres, gaps, target genes, etc. You can display these areas on the picture by submitting the corresponding annotation file.
Help
SYNOPSIS
GenomeSyn [options] align.coords
Options:
-help brief help message
-man full documentation
OPTIONS
-genomenumber/-gn
Draw main image of double/three sequence alignment, value is 2/3,
default true(2), that is default output double sequence alignment
chart.
-aligntype/-at
In the three-sequence alignment (ie "-genomenumber 1") choose to
draw the three-sequence alignment heatmap, value is 1/2/3, default
fault(1), that is default not output the heatmap of the
three-sequence alignment.
-curveto/-curve
Draw synteny blocks with curve or straight line, value is 1/0,
default true(1), that is default output as a curve.
-highlightinversion/-highlight
Highlight inversion, value is 1/0, default true(1), that is
default the inverted information is highlighted.
-SVG_PDF/-pdf
Format transition, generate the corresponding PDF format file with
the SVG format file as the original, value is 1/0, default
true(1), that is default output SVG format and PDF format files
are output at the same time.
-chromosomenumber1/-n1
Set the number of chromosomes in genome1 (ie reference genome),
eg. 12
-chromosomenumber2/-n2
Set the number of chromosomes in genome2 (ie query genome), eg. 12
-chromosomenumber3/-n3
Set the number of chromosomes in genome number three (ie query
genome2), eg. 12
-illustration/-i
Draw illustration, value is 1/0, default true(1).
-genomeSeq1/-g1
Input the genome1 fasta file to obtain the length of each
chromosome in the genome1.
-genomeSeq2/-g2
Input the genome2 fasta file to obtain the length of each
chromosome in the genome2.
-genomeSeq3/-g3
Input the genome3 fasta file to obtain the length of each
chromosome in the genome3.
-comparison_file/-comparison_file1/-cf1
Input the coordinate file for comparing genome1 and genome2, if
there is no coordinate file, call mummer to compare genome1 and
genome2 to generate this coordinate file, such as
referencevsquery1.delta.filter.coords.
-comparison_file2/-cf2
Input the coordinate file for comparing genome1 and genome3, if
there is no coordinate file, call mummer to compare genome1 and
genome3 to generate this coordinate file, such as
referencevsquery2.delta.filter.coords.
-comparison_file3/-cf3
Input the coordinate file for comparing genome2 and genome3, if
there is no coordinate file, call mummer to compare genome2 and
genome3 to generate this coordinate file, such as
query1vsquery2.delta.filter.coords.
-centromere_genome1/-centromere1
Input the centromere position file of genome1, the file uses the
bed (Browser Extensible Data) format, and draw centromeres on each
chromosome of genome1.
-centromere_genome2/-centromere2
Input the centromere position file of genome2, the file uses the
bed (Browser Extensible Data) format, and draw centromeres on each
chromosome of genome2.
-centromere_genome3/-centromere3
Input the centromere position file of genome3, the file uses the
bed (Browser Extensible Data) format, and draw centromeres on each
chromosome of genome3.
-telomere_genome1/-telomere1
Input the telomere position file of genome1, the file uses the bed
format, and draw telomere on each chromosome of genome1.
-telomere_genome2/-telomere2
Input the telomere position file of genome2, the file uses the bed
format, and draw telomere on each chromosome of genome2.
-telomere_genome3/-telomere3
Input the telomere position file of genome3, the file uses the bed
format, and draw telomere on each chromosome of genome3.
-snp_genome1/-snp1
Input the SNP file of genome1, which uses the bed format to map
the SNP distribution of genome1.
-snp_genome2/-snp2
Input the SNP file of genome2, which uses the bed format to map
the SNP distribution of genome2.
-snp_genome3/-snp3
Input the SNP file of genome3, which uses the bed format to map
the SNP distribution of genome3.
-TE_genome1/-TE1
Input the TE file of genome1, which uses the bed format to map the
TE distribution of genome1.
-TE_genome2/-TE2
Input the TE file of genome2, which uses the bed format to map the
TE distribution of genome2.
-TE_genome3/-TE3
Input the TE file of genome3, which uses the bed format to map the
TE distribution of genome3.
-PAV_genome1/-PAV1
Input the PAV file of genome1, which uses the bed format to map
the PAV distribution of genome1.
-PAV_genome2/-PAV2
Input the PAV file of genome2, which uses the bed format to map
the PAV distribution of genome2.
-PAV_genome3/-PAV3
Input the PAV file of genome3, which uses the bed format to map
the PAV distribution of genome3.
-NLR_genome1/-NLR1
Input the NLR file of genome1, which uses the bed format to map
the NLR distribution of genome1.
-NLR_genome2/-NLR2
Input the NLR file of genome2, which uses the bed format to map
the NLR distribution of genome2.
-NLR_genome3/-NLR3
Input the NLR file of genome3, which uses the bed format to map
the NLR distribution of genome3.
-gene_density_genome1/-GD1
Input the annotation file of genome1, which uses the gff3 format
to map the gene density distribution of genome1.
-gene_density_genome2/-GD2
Input the annotation file of genome2, which uses the gff3 format
to map the gene density distribution of genome2.
-gene_density_genome3/-GD3
Input the annotation file of genome3, which uses the gff3 format
to map the gene density distribution of genome3.
-targetgene_genome1/-targetgene1
Input the target gene file of genome 1, the file uses the bed
format, the target gene can be any gene that the user studies.
-targetgene_genome2/-targetgene2
Input the target gene file of genome 2, the file uses the bed
format, the target gene can be any gene that the user studies.
-targetgene_genome3/-targetgene3
Input the target gene file of genome 3, the file uses the bed
format, the target gene can be any gene that the user studies.
-targetgene_name/-targetgene
Set the name of the target gene, default output as "Target Gene".
-output1/-o1
Set the name of output SVG format file1, default
GenomeSyn-main-1.svg.
-output2/-o2
Set the name of output SVG format file2, default
GenomeSyn-main-2.svg.
-output3/-o3
Set the name of output SVG format file3, default GenomeSyn
heatmap.svg.
-output4/-o4
Set the name of output SVG format file4, default GenomeSyn
identity.svg.
-output5/-o5
Set the name of output SVG format file5, default GenomeSyn
coverage.svg.
-output6/-o6
Set the name of output SVG format file6, default GenomeSyn
heatmap2.svg.
-headline_identity/-headline1
Set the title of illustration1, default output is "GenomeSyn
identity".
-headline_coverage/-headline2
Set the title of illustration2, default output is "GenomeSyn
coverage".
-headline_heatmap/-headline3
Set the title of illustration3, default output is "GenomeSyn
heatmap".
-referencename/-reference/-ref
Set the name of the genome1, default output is "reference".
-queryname/-queryname1/-query/-query1
Set the name of the genome2, default output is "query"/"query1".
-queryname2/-query2
Set the name of the genome3, default output is "query2".
-chromosomename/-cn
Show the actual chromosome sort number in the comparison file,
value is 1/0, default fault(0), that is not to display, output
with a unified number.
-icon Whether to output the main image 1 icon, value is 1/0, default
true(1).
-genome1_color/-color1
Set the drawing color of the chromosome in genome1,default color
is LightBlue (#3979BC), recommended to input in hexadecimal color
code or RGB code, eg. "#3979BC"/"rgb(57,121,188)".
-genome2_color/-color2
Set the drawing color of the chromosome in genome2,default color
is Green(#499272), recommended to input in hexadecimal color code
or RGB code, eg. "#499272"/"rgb(73,146,114)".
-genome3_color/-color3
Set the drawing color of the chromosome in genome3, default color
is DarkBlue(#447784), recommended to input in hexadecimal color
code or RGB code, eg. "#447784"/"rgb(68,119,132)".
-synteny_color/-color4
Set the drawing color of the synteny blocks, default color is
LightGray(#DFDFE1), recommended to input in hexadecimal color code
or RGB code, eg. "#DFDFE1"/"rgb(223,223,225)".
-inversion_color/-color5
Set the drawing color of the inversion blocks, default color is
DarkOrange(#E56C1A), recommended to input in hexadecimal color
code or RGB code, eg. "#E56C1A"/"rgb(229,108,26)".
-translocation_color/-color6
Set the drawing color of the translocation blocks, default color
is Saffron(#EFCF48), recommended to input in hexadecimal color
code or RGB code, eg. "#EFCF48"/"rgb(239,207,72)".
-centromere_color/-color7
Set the drawing color of the centromere blocks, default color is
Orange(#E4993F), recommended to input in hexadecimal color code or
RGB code, eg. "#E4993F"/"rgb(228,153,63)".
-telomere_color/-color8
Set the drawing color of the telomere blocks, default color is
Purple(#441680), recommended to input in hexadecimal color code or
RGB code, eg. "#441680"/"rgb(68,22,128)".
-PAV_color/-color9
Set the drawing color of PAVs, default color is
LightYellow(#F9F067), recommended to input in hexadecimal color
code or RGB code, eg. "#F9F067"/"rgb(249,240,103)".
-NLR_color/-color10
Set the drawing color of the NLRs, default color is Cyan(#00FFFF),
recommended to input in hexadecimal color code or RGB code, eg.
"#00FFFF"/"rgb(0,255,255)".
-SNP_color/-color11
Set the drawing color of the SNPs, default color is
DoderBlue(#1E90FF), recommended to input in hexadecimal color code
or RGB code, eg. "#1E90FF"/"rgb(30,144,255)".
-genedensity_color/-color12
Set the drawing color of the SNPs, default color is
DarkGreen(#368F5C), recommended to input in hexadecimal color code
or RGB code, eg. "#368F5C"/"rgb(54,143,92)".
-targetgene_color/-color13
Set the drawing color of the targetgene, default color is
Crimson(#DC143C), recommended to input in hexadecimal color code
or RGB code, eg. "#DC143C"/"rgb(220,20,60)".
-help/? Print a brief help message and exits.
-man Prints the manual page and exits.
Python
This version provides some of the most basic functions, including centromeres, telomeres, gaps, and does not integrate MUMmer. When you only need a simple synteny analysis or only a small amount of annotation information, it is recommended that you use this version.
Help
*****The parameters with an asterisk must be filled in.*****
[-h/—help]
—Get help.
*[-t/—picturetype]
—Choose the type of picture you want.
*[-a/—firstfile]
—The first mummer file.
[-b/—secondfile]
—The second mummer file.
[-c/—imporvementregin1]
—The imporvementregin file corresponding to the first query Seq.
[-d/—imporvementregin2]
—The imporvementregin file corresponding to the reference Seq.
[-w/—imporvementregin3]
—The imporvementregin file corresponding to the second query Seq .
[-e/—centromere1]
—The centromere file corresponding to the first query Seq.
[-f/--centromere2]
—The centromere file corresponding to the reference Seq.
[-g/—centromere3]
—The centromere file corresponding to the second query Seq .
[-i/—telomere1]
—The telomere file corresponding to the first query Seq.
[-j/—telomere2]
—The telomere file corresponding to the reference Seq.
[-k/—telomere3]
—The telomere file corresponding to the second query Seq.
*[-l/—genomeSeq1]
—The first query Seq.
*[-m/—genomeSeq2]
—The reference Seq.
[-n/—genomeSeq3]
—The second Seq.
[-o/—heatmap]
—Generate heatmap.[t/f]
[-p/—statistics]
—Generate Statistical graph.[t/f]
*[-r/—output]
—The path of the output file.
*[-s/—imageFormats]
—The format of the generated picture.
*[-q/—targetChr]
—Chromosome number of the first query Seq.
*[-u/—targetChr2]
—Chromosome number of the reference Seq.
[-v/—targetChr3]
—Chromosome number of the second query Seq.