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Hi Linxing:
Thank you for developing this nice tool! I am curious about what's the functions does COBRA have in the classic virome pipeline as it's a new software.
For example, I used MEGAHIT to get…
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Identifies fusion proteins from RNAseq and also catches expression of viral sequences:
https://github.com/ndaniel/fusioncatcher
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I'm not sure if this is something we want to fix or just something we want to note (can be a real issue for some viral sequences) but sequences with large numbers of Xs or other non-residue characters…
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Reduce the chance of erroneously depleting viral or bacterial sequences that have remote homology to human.
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Hi,
I am trying to create a database to run on a PC containing bacterail archaeal and viral reads.
The aim is to be able to run centrifuge and pavian offline to support ONT sequencing in the field…
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Hello I'm trying to create the standard Kraken 2 database, with the following command:
kraken2-build --standard --threads 16 --db kraken-Sdb
I'm getting this:
Step 1/2: Performing rsync file …
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Experiment: Single Cell RNAseq from 10x genomics
File Format: I have 2 Lanes (L001 and L002) and I also have for each of the lanes an R1 and R2 file
Reference Genome: Multiple HIV proviral sequences…
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I am getting following error:
Thu Feb 17 07:53:17 UTC 2022: Identifying viral sequences
Thu Feb 17 07:53:18 UTC 2022: Treating 0 reference sequences as viral sequences.
Thu Feb 17 07:53:58 UTC 20…
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Hi, I'm trying to download the viral-neighbors db from NCBI, but the download halts with this message. Could you help on that?
```
krakenuniq-download --db $DBDIR viral-neighbors --threads 10
Do…
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Gherman, I was wondering - if a viral sequence were present in a sample, would it end up in the cleaned reads (to be sorted out later)? The READ QA folder only contains human sequences pulled out of …