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iqbal-lab-org
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pandora
Pan-genome inference and genotyping with long noisy or short accurate reads
MIT License
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release: release version 0.12.0-alpha.0
#355
leoisl
closed
6 months ago
0
Sync dev to master, preparing for release 0.12.0-alpha.0
#354
leoisl
closed
6 months ago
0
feat: adding param --partial-matching-lower-bound to pandora map, discover and command subcommands
#353
leoisl
closed
6 months ago
0
feat: adds flag --no-gene-coverage-filtering to pandora map, compare and discover
#352
leoisl
closed
6 months ago
0
feat: adds parameter --min-gene-coverage-proportion to pandora map, compare and discover
#351
leoisl
closed
6 months ago
0
Remove kmer_covgs.txt and kmer_probs.txt from pandora map/compare output
#350
leoisl
opened
7 months ago
0
Downgrade log level from warning to info for "[warning] Could not find reference sequence for <gene> in the PRG so using the consensus path"
#349
leoisl
opened
8 months ago
0
Add parameter allowing pandora to filter out genes that are not proportionally covered enough by the reads
#348
leoisl
closed
6 months ago
4
Pandora mapping is slow
#347
iqbal-lab
opened
8 months ago
4
Can I use Pandora to do de novo local assembly of regions that have no read coverage when doing a mapping to reference?
#346
Isoris
closed
10 months ago
3
Merge dev into master - prepare for release v0.11.0-alpha.0
#345
leoisl
closed
10 months ago
1
Improved mapping
#344
leoisl
closed
6 months ago
5
Fix to finding the longest path through PRGs
#343
leoisl
closed
11 months ago
5
Index optimisation
#342
leoisl
closed
11 months ago
0
Add seed parameter for the random subcommand
#341
leoisl
opened
11 months ago
0
Remove --max-covg param
#340
leoisl
opened
11 months ago
0
Misc improvements before index optimisation PR
#339
leoisl
closed
11 months ago
1
How to treat the genomes which come from the same source? for instance if three samples are biological replicates.
#338
Isoris
opened
11 months ago
2
Clean up unused modules and remove read information bookkeeping
#337
leoisl
closed
11 months ago
2
Refactor common default CLI argument values
#336
leoisl
opened
11 months ago
0
Adds parameters dealing with auto-updating error rate and kmer model, and for gene filtering based on coverage
#335
leoisl
closed
11 months ago
10
Investigate making pandora to compile on Mac
#334
leoisl
opened
1 year ago
2
Incorrect mapping of a read to an incorrect gene as the true gene has no minimizer hits (with minimal example)
#333
Danderson123
opened
1 year ago
0
Incorrect annotation of one gene as another due to tight clustering of minimizer hits (with minimal example)
#332
Danderson123
opened
1 year ago
1
Lazy loading
#331
leoisl
closed
1 year ago
2
Logging: new optimisations and 4-way results
#330
leoisl
closed
10 months ago
9
Issue while choosing the reference path for genotyping
#329
AmayAgrawal
opened
1 year ago
4
Improving cluster size threshold choice
#328
leoisl
opened
1 year ago
1
Error adding hits to kmer graph: minimizer hit kmer node is invalid
#327
mbhall88
closed
1 year ago
3
Typo/bug maybe?
#326
iqbal-lab
closed
1 year ago
1
Pandora heavily undermapping
#325
leoisl
closed
6 months ago
3
Inferred VCF ref for a PRG does not match a start-to-end PRG path
#324
leoisl
opened
1 year ago
0
Runtime for pandora compare
#323
AmayAgrawal
opened
1 year ago
6
Strange genotype selection
#322
mbhall88
closed
1 year ago
10
allow confidence to equal threshold
#321
mbhall88
closed
1 year ago
0
Slight issue with checking minimum genotype confidence threshold
#320
mbhall88
closed
1 year ago
2
Add --compression-level parameter to pandora index subcommand
#319
leoisl
opened
1 year ago
0
Changing pandora index format
#318
leoisl
closed
1 year ago
2
Understanding Genotype output in the VCF file generated using Pandora map and compare
#317
AmayAgrawal
opened
1 year ago
6
Investigate pandora failing to map reads at the edge of a gene
#316
leoisl
opened
1 year ago
3
Improve pandora discovery RAM usage
#315
leoisl
opened
1 year ago
1
Prepare 0.10.0-alpha.0 release
#314
leoisl
closed
1 year ago
0
Misc changes for 0.10.0-alpha.0 release
#313
leoisl
closed
1 year ago
2
Broad roadmap of next features
#312
leoisl
opened
1 year ago
3
Improving indexing and mapping performance with low cost
#311
leoisl
opened
1 year ago
3
Make release for racon denovo branch
#310
leoisl
closed
1 year ago
11
Exploring removing path from pandora index and on-demanding loading of PRGs
#309
leoisl
opened
1 year ago
0
Remove `merge_index` command
#308
leoisl
closed
1 year ago
5
Upgrading pandora required c++ version from c++11 to c++14
#307
leoisl
closed
1 year ago
4
Refactor pandora index into a single, self-contained file
#306
leoisl
closed
1 year ago
13
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