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hoelzer-lab
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ribap
A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
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Improve RIBAP output for core/shell/cloud with varying cutoffs
#60
hoelzer
opened
1 month ago
0
Process `RIBAP:ilp_refinement (8)` terminated with an error exit status (1)
#59
Andrewab9
opened
5 months ago
1
Process `RIBAP:mmseqs2tsv` terminated with an error exit status (1)
#58
GabrieleRigano99
opened
6 months ago
12
Focus RIBAP analysis on a smaller set of target genes, screening more genomes
#57
hoelzer
opened
10 months ago
0
Calculate core gene tree
#56
hoelzer
closed
1 month ago
1
Hot fix for issue #54, skipping tree calc if no core gene MSA
#55
hoelzer
closed
10 months ago
5
RIBAP:filter_alignment failed
#54
bharat1912
closed
1 month ago
5
remove unnecessary gunzip
#53
hoelzer
closed
11 months ago
1
Error executing process > 'ilp_build (27)'
#52
bharat1912
closed
11 months ago
3
Update README.md
#51
lisa-mariebarf
closed
1 year ago
0
Example data
#50
hoelzer
closed
1 year ago
0
Chunk size
#49
hoelzer
opened
1 year ago
1
Automatically adjust the height/width of the UpSetR plot
#48
hoelzer
opened
1 year ago
0
Output folder names
#47
hoelzer
closed
1 year ago
1
IQTree resources
#46
hoelzer
closed
1 year ago
3
non-unique prokka IDs if input sequences are identical
#45
klamkiew
opened
1 year ago
2
Prokka fails with input genomes containing a dot ('.') in their file names
#44
klamkiew
closed
1 year ago
3
combine ILP results only with 95-roary call
#43
klamkiew
closed
1 year ago
0
IQ-TREE failing for test data set
#42
hoelzer
closed
1 year ago
10
Disk space
#41
hoelzer
closed
1 year ago
4
Dev into main; version0.8? 1.0?
#40
klamkiew
closed
1 year ago
7
conda environment of roary is not resolving
#39
klamkiew
closed
1 year ago
9
Estimate model per MSA and then design phylogeny run
#38
hoelzer
closed
1 year ago
2
add auto option for RAXML-NG max CPUs on HPC, hopefully also works local…
#37
hoelzer
closed
2 years ago
2
add prokka param for additional gbk file
#36
hoelzer
closed
2 years ago
0
Start ribap from own annotation
#35
lisa-mariebarf
opened
2 years ago
1
Run Prokka with reference annotation
#34
lisa-mariebarf
closed
2 years ago
4
Dev
#33
hoelzer
closed
2 years ago
0
Merge pull request #31 from hoelzer-lab/dev
#32
hoelzer
closed
2 years ago
0
Dev
#31
hoelzer
closed
2 years ago
0
update dev
#30
hoelzer
closed
2 years ago
0
up prokka
#29
hoelzer
closed
3 years ago
0
Align a lot of genomes
#28
hoelzer
closed
1 year ago
1
supervenn viz
#27
hoelzer
opened
3 years ago
0
Interactive UpSet
#26
hoelzer
opened
3 years ago
0
Bakki Genome visualization
#25
hoelzer
opened
3 years ago
0
Deal with fragmented gene annotations from PROKKA
#24
hoelzer
opened
3 years ago
0
added rearrange script
#23
MarieLataretu
closed
3 years ago
2
HTML table searchable
#22
hoelzer
opened
4 years ago
0
IQ-Tree update
#21
hoelzer
closed
1 year ago
3
Additional annotation of hypothetical proteins
#20
hoelzer
closed
11 months ago
0
Link ILP output instead of copy
#19
hoelzer
closed
1 year ago
0
Merge pull request #15 from hoelzer-lab/dev
#18
hoelzer
closed
4 years ago
0
Write out complete Prokka output
#17
hoelzer
closed
4 years ago
1
filter mmseqs2 output?
#16
hoelzer
closed
4 years ago
0
Dev
#15
hoelzer
closed
4 years ago
0
Merge pull request #10 from hoelzer-lab/dev
#14
hoelzer
closed
4 years ago
0
Check output combine/ribap_roaryxx_summary.txt file
#13
hoelzer
closed
4 years ago
0
Wrongly assigned orthologous gene
#12
hoelzer
closed
4 years ago
1
GLPSOL: Multiple use of variable 'x_A1h_A1t' not allowed
#11
hoelzer
closed
1 year ago
3
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