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Hi!
I'm using RESPECT to evaluate 10 octopus genomes - genomes that are expected to be human-sized or larger and repeat rich. Years ago people thought the genomes would be duplicated - but this has…
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Looking at a very high coverage nanopore sample, we have found a good example where there is a very high confidence call, in agreement with phenotype, but which is below the dynamically calculated thr…
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## Testing the effect of error profile on quantification.
As we noticed that there was a quite precise 2 factor error in kmer quantification we tried investigating this.
It was also pointed ou…
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Hello,
I am trying to use remora with megalodon, anyway when I run the "model train" command I get this error:
```
remora model train /data/Nanopore//Remora/remora_train_chunks.npz --model…
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Dear developers!
`./sortmerna --ref Silva_LSU_SSU.fasta --reads 13_1.fq.gz 13_2.fq.gz --aligned With_rRNA --other Clean --fastx --threads 8 -v --task 4`
[process:1460] Processing option: threads …
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Hi @voichek,
Thank you for this super useful approach and your paper was also pretty interesting to read. I have a question regarding to heritability results generated by EMMA (find in `EMMA_perm.…
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Hello,
I made custom kraken2 and Bracken databases following your tutorial, where I added several genomes to the pre-built GTDB Struo2 databases (thank you for providing these, by the way!). Howeve…
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The genome with which we are working is on snake genome, from Genus Indotyphlops. We have performed shallow sequencing or skim-sequencing on the genome of this organism. We wanted to estimate the plo…
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Hello,
I have been using pggb for a while now and over a couple of different builds. I have been able to run it previously and can still run a previous version (pulled February 8) without seeing thi…
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I'm working with a very repeat-rich fungal genome, with expected haploid genome size around 70 - 80 Mb. Genoscope seems to be locking onto the second (repeat-associated) peak and is producing a much l…