mummerplot results interpretation - Biostar: S mummer mummerplot alignment bash • 3 4k views ADD COMMENT • link 4 3 years ago by langziv utrif; 70 1 Entering edit mode Aside from the scattered dots, there is a clear vertical line for each contig scaffold It would suggest you have a array of repeats in these contigs Do you see this for every contig you have assembled? Also, you could
MUMmer plot visualization - Biostar: S Hi, I am using MUMmer plot to compare between a de novo assembly with reference genome The percent identity between two genomes is more than 99% but when I plot the two genomes with MUMmer plot, the plot (https: ibb co q08xsZw) doesn't look like that Does anyone have any idea? Thanks
Using MUMmer 3. 9. 4 I am trying to install MUMmer 3 9 4 on Ubuntu, following the instructions given here: https: github com gmarcais mummer blob master INSTALL md When I try to run nucmer, I get this error message: nucmer: error while loading shared libraries: libumdmummer so 0: cannot open shared object file: No such file or directory
mummer dot plot - Biostar: S You can use show-coords from MUMmer to check how many bases you should rotate the assembly (should be equal to the size of your small aligned fragment) I would also suggest to use dnadiff which is also part of MUMmer package
mummer plot interpretation - Biostar: S I want to know how to interpret the results of mummer plot graph? What is the meaning of different colours in the graph?
How to modify dot plot in MUMmer 3 for bacteria . . . - Biostar: S I would recommend using a different dot-plot visualizer for mummer output, one that is interactive and navigable my favorite: https: dnanexus github io dot see also: https: github com topics dotplot
A Result From Mummer Alignment I wonder what kind of alignment view you want or you need any specific format to parse with perl or python The usual way I do nucleotide alignment with mummer is following: align the two sequences nucmer -p out seq1 fa seq2 fa filter the results (delta format) delta-filter -g -u 95 out delta > out fil delta
How to convert MUMmer output to SAM, GFF, or any other . . . - biostars I am aligning contigs against a reference genome and would like import the output of Nucmer-MUMmer as a track in GBrowse MUMmer uses its own idiosyncratic output formats (delta format), and to my surprise I was unable to find any working parser for Mummer in BioPerl or BioPython
How to use mummers output for visualization - biostars. org Hi, I am using mummer for alignment and snp calling Now I have my list of snps but I am stuck at this current step which is to visualize the coverage of the sequence This is to confirm that the snps are really snps not some background noise or other factor