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I noticed that AA can work with tumor-only WGS data since it was tested on the cell line data. I am just wondering what would be the benefits if giving with paired normal WGS as well.
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Hi,
I'm experimenting with running COMPASS (using CNVs) with multiple samples (3 samples), where the cells then come from different runs with MissionBio. A problem is that they got sequenced at dif…
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Hi all,
The read_clustering step failed for whole operons (16S-ITS-23S, ~4.1k mean read length).
The whole nextflow pipeline ran through without errors (on a Mac M1) with test fastq files `mock4…
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I run cojac on wastewater samples which are sequenced using NimagenV3 primer amplicons. It worked well for most variant profile however I encountered this error while using a profile which has co-occu…
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Dear authors,
Thank you for your work, I was testing your software on several datasets and I obtained this error message:
```
[raven::] loaded 9004 sequences 0.110631s
[raven::Graph::Construct] …
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Somehow I'm ending up with a very low number of duplex reads after using Dorado duplex basecalling with the following command (used the ligation sequencing kit V14 SQK-LSK114):
`dorado duplex dna_r…
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Hi,
I had a run with primer designer with this parameters:
Strangely, in the result, the amplicon is built over the starting point of the region. Which sequence would the pipeline take in su…
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Hi there,
I have two questions:
1. You have mentioned that "ONTbarcoder has been optimized for protein coding gene like COI. While **there are ways** to obtain consensus for length variable non …
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Hi, I am trying out Ampligone. It works fast but I got a few questions. I am working with Nanopore reads of 16s rRNA amplicons.
1) If you provide the tool with a single reference, than it determine…
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I suggest using the poreCov pipeline as the backend for SARS-CoV-2 wastewater lineage deconvolution from nanopore long reads. You already added `freyja` ( #274 #270), which is great as the current com…