Kaisa Thorell

Hi! Would it be possible to include the option to use a nucleotide fasta that should be searched for explicitly rather than translated with promer for the organisms that does...

Hi! I am trying to recreate the pca plots generated by the sleuth `plot_pca` function with ggplot so that I can use more aesthetics functions but I cannot find out...

Hi! There is a typo in the panGWAS_user_manual.pdf, unfortunately in the Usage Example ;) Rscript /path/of/make_pangenome.r –contigFile contigs.txt –prodigal yes – similarity 0.7 –coverage 0.7 –prefix test –externaSoftwarePaths soft.txt externaSoftwarePaths...

I just ran BACTpipe over ~70 samples and for some Kraken failed due to out of memory problems. Unfortunately this means prokka didn't run either. I think we should change...

Include config file for large raw files?

11

I just bumped into the issue of having excessively large raw fastq files per sample which leads to that `fastp` times out with the current allocations in the rackham config....

Update citation/publish pipeline

25

With the 3.0 release we should update the Zenodo citation so that the correct people are acknowledged. Should we also try to publish the pipeline as some kind of short...

To add the possibility of performing hybrid assemblies of Nanopore/PacBio and Illumina data using `hybridSPAdes` would be nice. Need to think through how much of data preprocessing that needs to...