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JustinChu
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JupiterPlot
A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.
GNU General Public License v3.0
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Synteny graph not representing alignment results: I appreciate your help
#48
BioJules
closed
3 weeks ago
12
Labels
#47
aebaci
opened
2 months ago
2
can this pipeline be added to a container?
#46
KristinaGagalova
closed
3 months ago
4
CIRCOS ERROR cmd: circos -noparanoid -conf test.conf
#45
ykkim0127
closed
6 months ago
5
Problems with the aesthetics of the plot
#44
jacolmen
closed
3 months ago
1
Effect of mapping parameters
#43
tanpham15
closed
3 months ago
2
Request: Option to always show all contigs
#42
alexweisberg
closed
6 months ago
1
Can I retain some config files removed by your script?
#41
nzx9581
closed
6 months ago
2
Link files change chromosome names
#40
mpalmada
closed
1 year ago
0
No Y chromosome
#39
imdanique
closed
1 year ago
0
No links despite large regions of similarity visible in dot plot from MUMMER alignment
#38
mptrsen
closed
12 months ago
13
Reciprocity of matching regions
#37
ckeeling
closed
1 year ago
1
Set links between chromosomes
#36
Karimi-81
closed
6 months ago
2
Get chromosomal names/numbers on the "query", and alignment issue.
#35
siv-n
closed
12 months ago
4
Running failure
#34
JQVazquez
closed
3 years ago
2
Only a fraction of the represented scaffolds aligned to the reference.
#33
jprunier-ulaval
closed
6 months ago
4
output genome coverage
#32
aafshinfard
closed
2 years ago
0
output genome coverage
#31
aafshinfard
closed
3 years ago
0
correct .PRECIOUS files
#30
aafshinfard
closed
3 years ago
0
Fix problems on Mac OS
#29
JustinChu
closed
6 months ago
1
max number of scaffs to plot
#28
aafshinfard
closed
4 years ago
0
chromosome has no alignments!
#27
drashwinelkar
closed
4 years ago
5
circos plotting error
#26
mjmillerlab
closed
4 years ago
4
README.md: typo fixes
#25
jwcodee
closed
4 years ago
0
Add option to render the scaffold IDs or equivalent
#24
JustinChu
closed
1 year ago
1
Add option to change minimum MAPQ to be shown on plot
#23
JustinChu
closed
4 years ago
1
Change path for Samtools
#22
wlaw13
closed
4 years ago
3
Reg: Some maintenance of the tool
#21
harish0201
closed
5 years ago
2
numbers of scaffold to render & their order
#20
scintilla9
closed
4 years ago
2
Change color of the output and replot
#19
scintilla9
closed
5 years ago
2
Change labels and re-plot
#18
gbdias
closed
5 years ago
2
Add option to reorder reference and scaffolds iteratively
#17
JustinChu
closed
6 months ago
1
Add option to remove chr names from output
#16
JustinChu
closed
1 year ago
1
Add additional columns to seqOrder to show intended (median) location of alignment of scaffolds
#15
JustinChu
closed
6 months ago
2
Add option to place overlapping contigs
#14
JustinChu
closed
6 months ago
1
List of non-standard modules needed
#13
ckeeling
closed
6 years ago
1
Experiment with minimap2 alignments
#12
JustinChu
closed
5 years ago
0
Add option to easily change alpha of links
#11
JustinChu
closed
1 year ago
1
Add option to allow for poor alignments to be used in visualization
#10
JustinChu
closed
2 years ago
1
Add mode to intentionally drop out congruent links
#9
JustinChu
closed
6 months ago
1
Create a demo with example assembly and reference file inputs
#8
JustinChu
closed
2 years ago
0
Allow for scaffold names to be printed using an option
#7
JustinChu
closed
6 years ago
1
Script error: Can't use an undefined value as an ARRAY reference
#6
JustinChu
closed
7 years ago
2
recipe failure for the bed file
#5
mroach-awri
closed
7 years ago
7
Show poorly aligned regions of the scaffold with some sort of mark (like how gaps are shown)
#4
JustinChu
closed
6 months ago
1
Allow more global alignment solution to be used
#3
JustinChu
closed
6 years ago
1
Show inversions relative to predominate orientation by twisting link
#2
JustinChu
closed
6 years ago
1
Generate Make File-like workflow for generating intermediate files
#1
JustinChu
closed
7 years ago
0