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.