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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
368
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PGGB get the fasta file of non reference sequence
#267
ld9866
closed
1 year ago
0
update abpoa/smoothxg
#266
AndreaGuarracino
closed
1 year ago
0
Use `-Ofast` everywhere
#265
AndreaGuarracino
closed
1 year ago
0
Sandybridge o2
#264
AndreaGuarracino
closed
1 year ago
2
fix the management of mandatory parameters
#263
AndreaGuarracino
closed
1 year ago
0
[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
#262
LiaOb21
closed
1 year ago
4
emphasize more that it is better to build docker locally
#261
AndreaGuarracino
closed
1 year ago
0
Document `partition-before-pggb`
#260
AndreaGuarracino
closed
1 year ago
0
Get the fasta file of non reference sequence
#259
ld9866
closed
1 year ago
0
Annotating the 1D pangenome graph visualisation with centromere coordinates
#258
brettChapman
closed
2 days ago
1
ValueError: too many values to unpack (expected 13)
#257
ld9866
closed
1 year ago
3
Question about the example "scerevisiae7.fasta.gz "
#256
ld9866
closed
1 year ago
1
About the result study
#255
ld9866
closed
1 year ago
4
Call variants first (if requested), then compute the statistics and visualizations later (if requested)
#254
AndreaGuarracino
closed
1 year ago
0
wfmash -Y option
#253
SAMtoBAM
closed
1 year ago
4
extracting node path-coverage information
#252
SAMtoBAM
closed
1 year ago
3
Fix an issue in iterable smoothxg by updating smoothxg
#251
subwaystation
closed
1 year ago
0
filter alignments with gap-compressed identity below `-p x 0.8`
#250
AndreaGuarracino
closed
1 year ago
0
Remove the `smoothxg` loop as it has been internalized in it
#249
AndreaGuarracino
closed
1 year ago
0
Emit tools' version in the LOG/YAML output
#248
AndreaGuarracino
closed
1 year ago
4
High heterogeneity in sequences identity
#247
lsoldini
opened
1 year ago
2
Allow optional graph normalization
#246
AndreaGuarracino
closed
1 year ago
1
Three chromosome take too long time
#245
zhqduan
closed
1 year ago
16
update seqwish and its compilation
#244
AndreaGuarracino
closed
1 year ago
0
Adding the `partition-before-pggb` script to perform sequence partitioning before `pggb`
#243
AndreaGuarracino
closed
1 year ago
0
Heavily rework and slightly fix the entire pggb script
#242
AndreaGuarracino
closed
1 year ago
1
force reference output in VCF
#241
colindaven
closed
1 year ago
2
gcc 11 docker
#240
ekg
closed
1 year ago
3
update wfmash
#239
ekg
closed
2 years ago
0
PGGB use case with hexaploidy genomes
#238
brettChapman
opened
2 years ago
1
unchop the GFAFfixed graph
#237
AndreaGuarracino
closed
2 years ago
0
update bugfixed `GFAffix`
#236
AndreaGuarracino
closed
2 years ago
0
update wfmash for better head/tail patching
#235
AndreaGuarracino
closed
2 years ago
0
update wfmash for better short/medium sequence alignment
#234
AndreaGuarracino
closed
2 years ago
0
add additional diagnostic viz displaying a vertically summarized view of the graph
#233
subwaystation
closed
2 years ago
0
DRB1-3123 example not producing a nice graph anymore after `biwflambda` update.
#232
subwaystation
closed
2 years ago
5
update to wfmash with biwflambda
#231
AndreaGuarracino
closed
2 years ago
0
update smoothxg with faster odgi sort/layout
#230
AndreaGuarracino
closed
2 years ago
0
GFA with no P lines
#229
sivico26
closed
1 year ago
5
empty VCF after running PanGenIe on the pggb assembly
#228
Overcraft90
closed
2 years ago
1
Setting -n to number of genomes, or number of genomes minus one?
#227
henrivkgt
closed
2 years ago
3
Building a genus pangenome case
#226
sivico26
opened
2 years ago
1
Error following tutorial for PGGB VCF evaluation
#225
brettChapman
closed
1 year ago
5
Reduce even more `docker`/`singularity` image size
#224
AndreaGuarracino
closed
2 years ago
0
Update `smoothxg` with improved `SPOA`'s portability (for Docker/Singularity and Bioconda)
#223
AndreaGuarracino
closed
2 years ago
0
`docker/singularity`: fix versioning, smaller image, update `vcflib`, and faster building
#222
AndreaGuarracino
closed
2 years ago
0
Command terminated by signal 4
#221
colindaven
closed
2 years ago
8
Automatically set thread count
#220
ekg
closed
2 years ago
0
Sample command from README.md fails and fix?
#219
colindaven
closed
2 years ago
2
Add `--version` flag to display the version of `pggb`
#218
AndreaGuarracino
closed
2 years ago
0
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