iqbal-lab-org/pandora

Issues

• Request for new release

  #356 opened 2 months ago by Danderson123
  1

• Issue while choosing the reference path for genotyping

  #329 opened a year ago by AmayAgrawal
  4

• Pandora heavily undermapping

  #325 opened 10 months ago by leoisl
  3

• Add parameter allowing pandora to filter out genes that are not proportionally covered enough by the reads

  #348 opened a year ago by leoisl
  4

• Remove kmer_covgs.txt and kmer_probs.txt from pandora map/compare output

  #350 opened a year ago by leoisl
  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 opened a year ago by leoisl
  0

• Pandora mapping is slow

  #347 opened a year ago by iqbal-lab
  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 opened a year ago by Isoris
  3

• Logging: new optimisations and 4-way results

  #330 opened a year ago by leoisl
  9

• How to treat the genomes which come from the same source? for instance if three samples are biological replicates.

  #338 opened a year ago by Isoris
  2

• Add seed parameter for the random subcommand

  #341 opened a year ago by leoisl
  0

• Remove --max-covg param

  #340 opened a year ago by leoisl
  0

• Refactor common default CLI argument values

  #336 opened a year ago by leoisl
  0

• Investigate making pandora to compile on Mac

  #334 opened a year ago by leoisl
  2

• Incorrect annotation of one gene as another due to tight clustering of minimizer hits (with minimal example)

  #332 opened a year ago by Danderson123
  1

• Incorrect mapping of a read to an incorrect gene as the true gene has no minimizer hits (with minimal example)

  #333 opened a year ago by Danderson123
  0

• Error adding hits to kmer graph: minimizer hit kmer node is invalid

  #327 opened a year ago by mbhall88
  3

• Runtime for pandora compare

  #323 opened 2 years ago by AmayAgrawal
  6

• Improving cluster size threshold choice

  #328 opened 2 years ago by leoisl
  1

• Improving indexing and mapping performance with low cost

  #311 opened 2 years ago by leoisl
  3

• SAM file discussion

  #300 opened 2 years ago by leoisl
  8

• Typo/bug maybe?

  #326 opened 2 years ago by iqbal-lab
  1

• Inferred VCF ref for a PRG does not match a start-to-end PRG path

  #324 opened 2 years ago by leoisl
  0

• Slight issue with checking minimum genotype confidence threshold

  #320 opened 2 years ago by mbhall88
  2

• Strange genotype selection

  #322 opened 2 years ago by mbhall88
  10

• Failed to find alternate path

  #293 opened 2 years ago by mbhall88
  4

• Add new command pandora subindex

  #305 opened 2 years ago by leoisl
  1

• Refactor pandora index into a single, self-contained file

  #306 opened 2 years ago by leoisl
  13

• Upgrading pandora required c++ version from c++11 to c++14

  #307 opened 2 years ago by leoisl
  4

• Remove `merge_index` command

  #308 opened 2 years ago by leoisl
  5

• Add --compression-level parameter to pandora index subcommand

  #319 opened 2 years ago by leoisl
  0

• Broad roadmap of next features

  #312 opened 2 years ago by leoisl
  3

• Understanding Genotype output in the VCF file generated using Pandora map and compare

  #317 opened 2 years ago by AmayAgrawal
  6

• Investigate pandora failing to map reads at the edge of a gene

  #316 opened 2 years ago by leoisl
  3

• Move CI from Travis and container building from Quay to GH actions

  #297 opened 2 years ago by leoisl
  3

• Make release for racon denovo branch

  #310 opened 2 years ago by leoisl
  11

• Improve pandora discovery RAM usage

  #315 opened 2 years ago by leoisl
  1

• Exploring removing path from pandora index and on-demanding loading of PRGs

  #309 opened 2 years ago by leoisl
  0

• Handling huge indexes with few GBs of RAM

  #304 opened 2 years ago by leoisl
  1

• Logging performance of de novo variant discovery with racon

  #303 opened 2 years ago by leoisl
  5

• Improve runtime of de novo variant discovery with racon

  #302 opened 2 years ago by mbhall88
  4

• Coarse-grained simulation and evaluation framework to evaluate pandora mapping

  #301 opened 2 years ago by leoisl
  4

• How to deal with ambiguous bases in reads

  #294 opened 2 years ago by mbhall88
  6

• How to improve performance for Illumina-based analysis of viral pangenome

  #291 opened 3 years ago by dandaman
  12

• Define loci sequences in VCF header

  #292 opened 3 years ago by leoisl
  4

• How does pandora handle paired-end Illumina data?

  #290 opened 3 years ago by dandaman
  2

• Linking against musl statically

  #289 opened 3 years ago by leoisl
  4

• Crash with pandora compare --clean

  #288 opened 3 years ago by kdm9
  1

• Data for the paper to test software

  #287 opened 3 years ago by jdeligt
  1

• Haplotype phasing and coverage info in VCF

  #286 opened 3 years ago by gavinmdouglas
  5