gtonkinhill panaroo issues

gtonkinhill / panaroo

An updated pipeline for pangenome investigation

MIT License

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issues

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Running panaroo with pgap created gb files

#316 erinyoung opened 3 days ago
0
Invalid file extension

#315 baromagnoli opened 1 week ago
0
Allow for deterministic MDS coordinates

#314 revinici opened 1 week ago
0
Visualizing Panaroo Results

#313 AzizHN opened 1 month ago
2
Some gene alignments in aligned_gene_sequences/ have fragmented entries

#312 mudymudy opened 1 month ago
1
Panaroo Processing Inquiry

#311 AzizHN closed 1 month ago
1
Broken error handling in multithread_codonalign_build

#310 revinici opened 1 month ago
1
Low number of genes as output

#309 AzizHN closed 1 month ago
1
panaroo merge does not produce combined_protein_CDS.fasta

#308 revinici closed 1 month ago
2
Sporadic KeyError exceptions raised during collapse_families

#307 revinici opened 3 months ago
4
Add functionality to batch gene alignments

#306 revinici closed 1 month ago
4
Update the gene name in results of panaroo by bakta

#305 mook-monk closed 2 months ago
1
How to find paralog gene sequence in pan_genome_reference.fa?

#304 mai-rui-gao closed 2 months ago
2
Potential bug in panaroo

#303 Hocnonsense closed 2 months ago
1
Get Multifasta or alignment for each CDSs

#302 nbat64 closed 2 months ago
1
Biopython deprecation error

#301 lucyjanekelly closed 1 month ago
4
Default CD-HIT length different percent different than displayed in help message

#300 Danderson123 closed 4 months ago
2
Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

#299 NickJD closed 1 month ago
12
"NameError: Duplicate entry!!!" with a specific GenBank genome

#298 qianxuans closed 4 months ago
1
provide separate gff and fasta files as input for panaroo

#297 sun-qibo closed 5 months ago
2
Not running with prokka generated gff files

#296 EdwinDNavarroMonserrat closed 4 months ago
4
Invalid file extension

#295 MHassanSaeed closed 4 months ago
1
Gene clusters annotation

#294 anaGaGa98 closed 4 months ago
1
Gene sequences alignment

#293 thorcs1 closed 5 months ago
2
What to do with "xx_refound_yy" items in gene matrix?

#292 Asylulan closed 6 months ago
0
Recovering gene coordinates

#291 theodorross closed 6 months ago
2
Panaroo run time

#290 anuradhasingh15 closed 4 months ago
4
Request for Assistance in Identifying Core Genome from Result Files

#289 2021JohnSheng closed 7 months ago
2
Query Regarding Discrepancy in Output Information for Dataset of 3245 GFF3 Files

#288 2021JohnSheng closed 7 months ago
2
Continue from concatenate_core_genome_alignments?

#287 qianxuans closed 7 months ago
4
cut-off of 100% aa identity not working properly

#286 memoriasresiduais closed 4 months ago
1
Cd-hit-est problem

#285 anagaga27 closed 3 months ago
5
Increase in processing time

#284 anagaga27 closed 7 months ago
4
build: convert setup.py based setup to pyproject.toml

#283 afuetterer closed 5 months ago
2
ci: run pytest tests in parallel

#282 afuetterer closed 5 months ago
0
ci: add pip cache in ci to speed up package installation

#281 afuetterer closed 5 months ago
1
ci: bump github actions versions

#280 afuetterer closed 7 months ago
0
Bakta GFFs with --remove-invalid-genes still throw 'invalid gene!' error, doesn't get to alignment

#279 amyecampbell closed 7 months ago
2
UnboundLocalError: local variable 'prot_outname' referenced before assignment

#278 fengyuchengdu closed 7 months ago
5
Genes missing in the pangenome reference fasta

#277 LucoDevro closed 8 months ago
2
Discrepency between final_graph.gml and gene_presence_absence.csv

#276 sydelstan closed 7 months ago
4
Example of missing AMR gene allele

#275 Danderson123 closed 7 months ago
5
Alternative start codon GTG translated as Val instead of Met

#274 cednotsed closed 7 months ago
5
Multithread codonalign bottleneck

#273 nzmacalasdair closed 8 months ago
0
Fix name length reversion

#272 nzmacalasdair closed 8 months ago
0
Overly-long gene names cause panaroo-extract-gene to fail

#271 cednotsed closed 8 months ago
3
Merge filename length fix

#270 nzmacalasdair closed 9 months ago
0
Wrong IDs in pangenome reference fasta

#269 LucoDevro closed 9 months ago
3
Can't use panaroo of reference genomes annotated with prokka

#268 AnnaLew closed 9 months ago
4
Fix panaroo-integrate args

#267 maxibor closed 9 months ago
2