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pangenome
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pggb
the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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make stats option consistent with help
#317
mbhall88
closed
1 year ago
1
Even if the genome is small, shouldn't too many samples be added to build the graph
#316
Wwwwwwwyc
opened
1 year ago
8
Heuristic `wfmash`
#315
AndreaGuarracino
closed
1 year ago
0
Problems with skipping the wfmash step
#314
Lucio-Yang
closed
1 year ago
8
Construct pangenome
#313
Daishoulu
closed
2 days ago
3
vcfwave not found
#312
aijigekoukou-shen
closed
2 days ago
3
Update `vcflib` to get the fixed `vcfwave`
#311
AndreaGuarracino
closed
1 year ago
0
Converting to a single connected component
#310
JoshuaDanielRubin
opened
1 year ago
2
Producing subgraphs of large pangenomes
#309
ASLeonard
closed
1 year ago
2
Problem with the ODGI 1D visualization by path orientation
#308
KopalliV
closed
2 days ago
6
Joining the Chromosome Alignments?
#307
zskey-zn
closed
1 year ago
2
Building a better pangenome
#306
GeorgeBGM
opened
1 year ago
25
bioconda is still broken
#305
AndreaGuarracino
closed
1 year ago
0
update smoothxg to avoid uncovered edges
#304
AndreaGuarracino
closed
1 year ago
0
update `smoothxg` with a working `odgi`
#303
AndreaGuarracino
closed
1 year ago
0
The graph does not look quite the same as the collinear results
#302
Wwwwwwwyc
closed
1 year ago
7
Command terminated by signal 11
#301
Sh1ne111
closed
2 days ago
10
vg deconstruct libgomp: Thread creation failed: Resource temporarily unavailable
#300
Wwwwwwwyc
closed
2 days ago
3
pggb graph contains uncovered edges
#299
danydoerr
closed
1 year ago
20
Run times slow with 76 genomes
#298
brettChapman
closed
9 months ago
13
gfa2evaluation
#297
subwaystation
opened
1 year ago
0
update tools
#296
AndreaGuarracino
closed
1 year ago
0
add tools for gfa2evaluation in Dockerfile
#295
subwaystation
closed
1 year ago
0
Current versions of smoothxg and pggb on bioconda incompatible
#294
lrvdijk
closed
1 year ago
5
Update README.md
#293
petersudmant
closed
1 year ago
1
Command terminated by signal 9
#292
Zoeyoungxy
opened
1 year ago
7
Running pggb with singularity fails
#291
RobinVanSchendel
closed
1 year ago
4
Support metric parameter suffixes
#290
ekg
closed
1 year ago
1
(standard_in) 1: syntax error
#289
Wwwwwwwyc
closed
1 year ago
3
pggb versioning info causing git dubious ownership problems
#288
colindaven
opened
1 year ago
0
vc deconstruct error - more sample names in header than sample fields
#287
jdamas13
closed
2 days ago
8
update gfaffix
#286
AndreaGuarracino
closed
1 year ago
0
Update wfmash
#285
AndreaGuarracino
closed
1 year ago
0
Richer SV Annotation
#284
mgperry
opened
1 year ago
0
update fixed `odgi paths` in `smoothxg`
#283
AndreaGuarracino
closed
1 year ago
0
Fix versioning
#282
AndreaGuarracino
closed
1 year ago
0
update smoothxg/odgi
#281
AndreaGuarracino
closed
1 year ago
0
update smoothxg to perform the POA on unique sequences
#280
AndreaGuarracino
closed
1 year ago
0
Add/remove one assembly (or more) from a pangenome graph
#279
LiaOb21
closed
1 year ago
2
Skip sequence partitioning?
#278
fangbohao
closed
2 days ago
2
Possible community detection bug
#277
subwaystation
opened
1 year ago
5
Current Bioconda release does not find python scripts
#276
subwaystation
closed
1 year ago
7
Executable scripts
#275
AndreaGuarracino
closed
1 year ago
0
plot also uncalled bases
#274
AndreaGuarracino
closed
1 year ago
1
Scripts folder added to /usr/local/bin/
#273
thomasraulet
closed
1 year ago
1
this hopefully fixes a problem with Nextflow
#272
subwaystation
closed
1 year ago
1
add partition-before-pggb to docker container
#271
thomasraulet
closed
1 year ago
1
interoperability with vg - error:[vg::SmallSnarlSimplifier] Invalid graph on iteration 0
#270
colindaven
closed
1 year ago
14
fix `block_length` management and tweaks defaults
#269
AndreaGuarracino
closed
1 year ago
0
Building a graph from fragmented assemblies
#268
evcurran
opened
1 year ago
0
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