Andreas Wallberg

Suggestions for optimization

3

Dear @oushujun, Thanks for a wonderful tool! I have run this on a very large LTR_FINDER dataset from a large genome and poked around a little in the code. I...

Short reads and few repeats called with Bonito in non-model PromethION data

1

Dear developers, Following a brief discussion on Twitter, I will here present some stats from comparing **Bonito 0.3.2** against **Guppy 4.2.2** (HAC and Fast) basecalls using an Nvidia RTX 3090...

Advice on multi-sample, multi-species, multi-contig analyses for both πN/πS and dN/dS

4

Dear @cwnelson88 , Thanks for implementing these solutions in these scripts! These are hugely time-saving for anyone interested in accomplishing gene-centered population genomics! I have some questions which I think...

Producing an index for a very large and very fragmented genome assembly

1

Dear developers, I would like to try out Whisper for mapping paired end short reads against a very large and fragmented genome assembly (100s of thousands of contigs). It is...

Dear developers, Is there any way to tell which reads map with good enough coverage/quality to be part of the model training? Is that list of reads saved anywhere in...

Dear developers, We are training our own models for non-model organisms using R9.4.1 data, focusing our efforts towards data associated with protein-coding genes. When we use bonito to basecall our...

Dear developers, We are applying your tool across nine species to test if there is stronger evidence of ancestral WGD in one species vs. the others. The tool is working...

Amino acid J?

1

Dear @ogotoh, I have mapped protein sequences to a genome and observe in the alignment output (O1) that many codons that I expect to encode "S" or Serine are written...

Dear all, I am working on a non-model species and wonder what particular considerations I should take for my analyses with this tool. For example, do the pre-made HMM-profiles apply...

VCFs - chromosome scale or local subsets?

3

Dear @pkalbers, Can you please advice on the structure of the input data? Lets say I am interested in the age distribution of haplotypes in divergent loci observed across the...