SoftBerry - sygraph

SyGraph

Web system for visualization of synteny alignments and comparison of assembly contigs
Build contains alignment using Genome Match or Nucmer software.

Example2: Opisthorchis felineus vs Clonorchis sinensis (GenomMatch format)

Paste alignment in GenomMath or Coords format:
L:318908 N:1 SW 559.187 SL 206.186 Sequence scaff_1 vs. 1411 Base sequences [clonorchis_sinensis.PRJDA72781.WBPS5.genomic-100kb.fa]. [DR] Sequence: 1086( 1), S: 142, L: 157881 scf01087 1-157881 Summ of blocks lengths: 850,Homology: 87.176 On Target sequence: start 279678, end 280606, length 929. On Query sequence: start 7041, end 7961, length 921. [DR] Sequence: 1086( 2), S: 142, L: 157881 scf01087 1-157881 Summ of blocks lengths: 1742,Homology: 90.987 On Target sequence: start 281957, end 283950, length 1994. On Query sequence: start 8691, end 10682, length 1992. [DR] Sequence: 1086( 3), S: 142, L: 157881 scf01087 1-157881 ...
Alternatively, load a local file with aligment:
Local file name:

Format of alignment:

Information about the length of the sequence
in the target file
scaff_1 318908 scaff_10 1206811 scaff_100 767532 scaff_101 588647 scaff_103 1838421 scaff_104 354617 scaff_1045 124000 scaff_105 1230429 scaff_106 1981972 scaff_107 857377 ...
Alternatively, load a local file:
Local file name:

Information about the length of the sequence
in the query file
scf00011 2050842 scf00005 1947747 scf00013 1543701 scf00001 1511247 scf00008 1502757 scf00006 1494832 scf00004 1489989 scf00010 1407960 scf00002 1342279 scf00007 1334318 ...
Alternatively, load a local file:
Local file name:

Coverage threshold between contigs/chrs:

Your use of Softberry programs signifies that you accept Terms of Use

Last modification date: 19 Oct 2016

Services Test Online

SyGraph

Example2: Opisthorchis felineus vs Clonorchis sinensis (GenomMatch format)