iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads

iqbal-lab-org/pandora Issues

Remove kmer_covgs.txt and kmer_probs.txt from pandora map/compare output
Updated 7 months ago
Downgrade log level from warning to info for "[warning] Could not find reference sequence for <gene> in the PRG so using the consensus path"
Updated 7 months ago
Add parameter allowing pandora to filter out genes that are not proportionally covered enough by the reads
Closed 6 months ago4
Pandora mapping is slow
Updated 8 months ago4
Can I use Pandora to do de novo local assembly of regions that have no read coverage when doing a mapping to reference?
Closed 9 months ago3
Add seed parameter for the random subcommand
Updated a year ago
Remove --max-covg param
Updated a year ago
How to treat the genomes which come from the same source? for instance if three samples are biological replicates.
Updated a year ago2
Refactor common default CLI argument values
Updated a year ago
Investigate making pandora to compile on Mac
Updated a year ago2
Incorrect mapping of a read to an incorrect gene as the true gene has no minimizer hits (with minimal example)
Updated a year ago
Incorrect annotation of one gene as another due to tight clustering of minimizer hits (with minimal example)
Updated a year ago1
Logging: new optimisations and 4-way results
Closed 10 months ago9
Issue while choosing the reference path for genotyping
Updated 5 months ago4
Improving cluster size threshold choice
Updated a year ago1
Error adding hits to kmer graph: minimizer hit kmer node is invalid
Closed a year ago3
Typo/bug maybe?
Closed a year ago1
Pandora heavily undermapping
Closed 6 months ago3
Inferred VCF ref for a PRG does not match a start-to-end PRG path
Updated a year ago
Runtime for pandora compare
Updated a year ago6
Strange genotype selection
Closed a year ago10
Slight issue with checking minimum genotype confidence threshold
Closed a year ago2
Add --compression-level parameter to pandora index subcommand
Updated a year ago
Understanding Genotype output in the VCF file generated using Pandora map and compare
Updated a year ago6
Investigate pandora failing to map reads at the edge of a gene
Updated a year ago3
Improve pandora discovery RAM usage
Updated 2 years ago1
Broad roadmap of next features
Updated a year ago3
Improving indexing and mapping performance with low cost
Updated a year ago3
Make release for racon denovo branch
Closed a year ago11
Exploring removing path from pandora index and on-demanding loading of PRGs
Updated 2 years ago
Remove `merge_index` command
Closed a year ago5
Upgrading pandora required c++ version from c++11 to c++14
Closed a year ago4
Refactor pandora index into a single, self-contained file
Closed a year ago13
Add new command pandora subindex
Closed a year ago1
Handling huge indexes with few GBs of RAM
Updated 2 years ago1
Logging performance of de novo variant discovery with racon
Updated 2 years ago5
Improve runtime of de novo variant discovery with racon
Closed 2 years ago4
Coarse-grained simulation and evaluation framework to evaluate pandora mapping
Updated 2 years ago4
SAM file discussion
Updated a year ago8
Move CI from Travis and container building from Quay to GH actions
Closed a year ago3
How to deal with ambiguous bases in reads
Closed 2 years ago6
Failed to find alternate path
Updated a year ago4
Define loci sequences in VCF header
Closed 2 years ago4
How to improve performance for Illumina-based analysis of viral pangenome
Updated 2 years ago12
How does pandora handle paired-end Illumina data?
Closed 2 years ago2
Linking against musl statically
Updated 2 years ago4
Crash with pandora compare --clean
Updated 2 years ago1
Data for the paper to test software
Updated 3 years ago1
Haplotype phasing and coverage info in VCF
Closed 3 years ago5
[Question] Could genotyping of SNPs of metagenomic reads work?
Closed 3 years ago2