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mikolmogorov
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Ragout
Chromosome-level scaffolding using multiple references
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ERROR: bad integers or strand in MAF (strand must be + for reference sequence) --
#89
chun-he-316
opened
6 months ago
2
Six is not supported in Python3.12. Isn't it time to drop Python2 compatibility
#88
tillea
opened
8 months ago
1
Does Ragout trim contigs' ends?
#87
touala
closed
11 months ago
2
How to check validity of results
#86
Alexkortsi
opened
1 year ago
1
Ragout is incompatible with Python 3.10
#85
aminakur
opened
1 year ago
1
When scaffolding against a high quality reference, what do outputs of "hybrid" scaffolds most likely indicate?
#84
DaRinker
opened
1 year ago
4
Help/advice trouble shooting a couple of problematic samples that ragout is tripping over
#83
DaRinker
closed
1 year ago
1
Best practices question--is "overfiting" to the reference sequence a problem?
#82
DaRinker
opened
1 year ago
3
Methods question with Ragout
#81
ChuChuChaddy
closed
1 year ago
1
slight confusion on inputs for cactus when then using in ragout
#80
benyoung93
closed
1 year ago
3
Phast error on MAF file produced by Ragout: strand must be + for reference sequence
#79
amizeranschi
closed
1 year ago
2
Interpretation of branch length in the inferred tree
#78
amizeranschi
closed
1 year ago
2
Unable to run Ragout
#77
sunnyEV
closed
2 years ago
1
Ragout error - TypeError: expected str, bytes or os.PathLike object, not NoneType
#76
ChuChuChaddy
opened
2 years ago
2
"N"s in the output files
#75
EllistonV
closed
1 year ago
1
multiple targets
#74
EllistonV
closed
3 years ago
1
Really new
#73
EllistonV
closed
3 years ago
1
Detecting chimeric adjacencies Error
#72
sajjadasaf
closed
3 years ago
2
ERROR: permutation ids
#71
ardy20
closed
3 years ago
5
Add architecture ppc64le to travis build
#70
ddeka2910
closed
3 years ago
1
AttributeError: 'Graph' object has no attribute 'node'
#69
damioresegun
closed
3 years ago
1
Sibeliaz .maf input leads to unidentified error in Ragout
#68
rstewa03
closed
4 years ago
3
Ragout unable to read target fasta file
#67
rstewa03
closed
3 years ago
3
Proposed fix for networkx removed function
#66
pmoulos
closed
4 years ago
5
dtype conversion in hal.py
#65
bernard-kim
closed
4 years ago
3
dtype conversion in hal.py
#64
bernard-kim
closed
4 years ago
1
AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs'
#63
drashwinelkar
closed
4 years ago
1
No synteny blocks found inspite of having block coverage of 89.86%
#62
drashwinelkar
closed
1 year ago
11
TypeError using HAL alingment
#61
stefjanson
closed
4 years ago
6
Required argument error with hal2mafMP.py
#60
bernard-kim
opened
4 years ago
7
Hal to Maf manual conversion
#59
sivico26
closed
4 years ago
5
Input is larger than 1 GB, can't proceed
#58
fergsc
closed
4 years ago
2
Problem with Ragout installed from Bioconda: ERROR: "ragout-maf2synteny" native module not found
#57
amizeranschi
closed
4 years ago
2
Cannot install following procedure
#56
enormandeau
closed
4 years ago
1
explicitely require bioconda channel for conda
#55
enormandeau
closed
4 years ago
1
output suggestion
#54
alantsangmb
closed
4 years ago
1
work flow stuck
#53
mostafaabuzaid25
closed
5 years ago
1
Please port to Python3
#52
tillea
closed
4 years ago
8
NetworkX 2.3 not supported
#51
ipetrushin
opened
5 years ago
7
Comparing variants detecting from Ragout genome and other variant calling tools
#50
hanbinlu
closed
5 years ago
1
Why is my scaffolded genome larger than the total contig length and my target genome?
#49
CristianRiccio
closed
5 years ago
1
Lowering the minimum size for sinteny blocks
#48
salvocamiolo
closed
5 years ago
2
ERROR: No sequences read for genome XXX. Check recipe for correctness ( Hal )
#47
shameem356
closed
5 years ago
1
hal2maf : --start and --length require --refSequenceName
#46
shameem356
closed
5 years ago
3
ERROR: "hal" is not installed.
#45
shameem356
closed
5 years ago
6
TypeError: 'instancemethod' object is not iterable
#44
lac2208
closed
5 years ago
3
Multiple Assemblers
#43
kokyriakidis
closed
5 years ago
2
ERROR: No sequences read for genome X (from HAL file).
#42
aprezvykh
closed
5 years ago
5
Make everything work with networkx >= 2.2.
#41
latticetower
closed
5 years ago
1
Alternative alignment tool
#40
RenzoTale88
opened
5 years ago
13
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