pandora

pandora copied to clipboard

Issue while choosing the reference path for genotyping

4

Hi, I am facing an issue regarding the reference path that pandora uses for genotyping the variants. It is basically using the less frequent supported path instead of most frequent...

AmayAgrawal

leoisl

Mabi got confused by this warning message, and I think the common use case for `pandora` is to actually not receive reference sequences for the genes and automatically infer it...

leoisl

Pandora mapping is slow

4

Placeholder as @Danderson123 keeps saying this and I don't want to lose it. Mapping reads from one sample to a PRG (Ecoli + a few thousand AMR genes) taking 30...

iqbal-lab

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

2

Hello, Thank you for making this useful tool, my question is the following, I would like to know, when i'm making a pangenome from diverse strains of Streptococcus iniae species,...

Isoris

leoisl

Downsampling reads is an upstream task, not pandora responsibility

leoisl

See Zam's comment at https://github.com/rmcolq/pandora/pull/335 Basically, we have several common default CLI args for `compare`, `map` and `discover`, see https://github.com/rmcolq/pandora/blob/master/include/compare_main.h https://github.com/rmcolq/pandora/blob/master/include/map_main.h https://github.com/rmcolq/pandora/blob/master/include/denovo_discovery/discover_main.h Would be better if there was a header...

leoisl

Investigate making pandora to compile on Mac

2

would make DrPrg accessible to more people

leoisl

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

1

Hey Leandro! I have been taking a look at cases where Pandora incorrectly annotates on gene as another. I took the first allele in each MSA that build my panRG...

Danderson123