Alexandra Weisberg

feature request: save load graph

3

Bandage is fantastic, I'm glad to hear you are continuing its development. I was wondering if it would be possible to implement a save/load feature? This would be useful for...

Error in genotype reading temporary input fasta

4

I've started a run of graphtyper with a command for each chromosome of my reference: graphtyper genotype --threads 16 --verbose --sams=bamlist --region=H1_8_48-4_1 REF.fna graphtyper genotype --threads 16 --verbose --sams=bamlist --region=H1_8_48-4_2...

support for haploid/different ploidy

1

Hi, I am really interested in using graphtyper for my bacterial genome SNP calling as there is a lot of diversity in some lineages and typical SNP calling pipelines run...

Macromolecular structure and integron annotation, custom features

2

**Is your feature request related to an existing issue or bug?** no **Is your new feature related to a general problem?** Typically annotation of large secretion systems (T3SS, T4SS, T6SS,...

Thanks for writing this tool, it works very well. I was wondering if it would be possible to add an option such that all contigs (query and ref) are shown,...

remote AntiSMASH fails with duplicate CDS features

1

**Are you using the latest release?** Version 1.8.14 **Describe the bug** Running the tutorial for genome+RNAseq with our own data, we successfully get through most of the annotation stages. However...

Hi, I am looking into an issue with a separate program that uses tape (https://github.com/zhangyumeng1sjtu/T4SEfinder/issues/2). I am running this program on a computing cluster that does not have a GPU,...

diamond makedb with tmpdir gives error after version 2.1.0

5

Hi, When I run diamond makedb with the --tmpdir parameter, I get the following error: diamond makedb --db test --in test.faa --tmpdir ./tmp `Error: Option is not permitted for this...

Hi, I just got guppy up and running on a machine with a 6000 Ada GPU. Here are the results of running it: gpu,gpu_memory,gpu_memory_used,gpu_driver_version,cuda_version,guppy_version,guppy_model,chunk_size,chunks_per_runner,num_basecallers,runners_per_device,samples_per_second NVIDIA RTX 6000 Ada Generation,49140,7043.38362,525.85.05,12.0,6.3.9+799d5bd,fast,2000,160,,,8.14516e+07 NVIDIA...

Hi, It seems that there are several places in the code where the user input number of threads is ignored and it just uses 10 or 20 by default. Additionally,...