mikolmogorov Ragout issues

mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references

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issues

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ERROR: bad integers or strand in MAF (strand must be + for reference sequence) --

#89 chun-he-316 opened 4 months ago
1
Six is not supported in Python3.12. Isn't it time to drop Python2 compatibility

#88 tillea opened 5 months ago
1
Does Ragout trim contigs' ends?

#87 touala closed 8 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 3 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 4 years ago
1
Please port to Python3

#52 tillea closed 4 years ago
8
NetworkX 2.3 not supported

#51 ipetrushin opened 4 years ago
7
Comparing variants detecting from Ragout genome and other variant calling tools

#50 hanbinlu closed 4 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 4 years ago
2
ERROR: No sequences read for genome XXX. Check recipe for correctness ( Hal )

#47 shameem356 closed 4 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