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I have a naive question about your MSA methodology. Why would the aligner choose to align short segments (1000bp) before aligning again? Perhaps I am misunderstanding the parameters to abPOA.
E…
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Hi,
I installed TideHunter by conda. chr9_sub.fa length is 0.5Mbp. The server memory size is 128G. TideHunter version is 1.5.3.
When I used command "TideHunter -f 2 chr9_sub.fa > chr9.cons.out" to…
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Hi,
I am very interested in experimenting with the pair decoding of bonito for our R2C2 data.
Two questions:
1) Is there still a way to produce .npy files required by poreover? Is seems like t…
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Hi,
Thank you for the cool package. I'd like to request "consensus view". That's when only the sequence of the reference (the top alignment) is visible with the rest hidden/replaced with a characte…
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I was wondering if I can generate a MAF (mutation annotation file) from a Fasta file which contains the consensus sequences of multiple samples. I ask, because I wanted a best way to define when mutat…
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Dear Wayne,
Every now and then I'm looking for freely available molecular biology software, e.g. to give it to our beginner students or use it by myself.
For my own little problems I'm actually u…
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Webservice that chooses a reference sequence based on
Input:
1) HLA (or other) consensus sequences. full length or features.
2) IMGT version.
Output:
1) Best matching reference sequence
2) …
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I have aligned contigs to longreads using Minimap2 and generated the paf file. I am trying to use racon to get a consensus of these.
The command I am using:
./racon PA_hifi.fa minimapConToHiFimappe…
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Hello,
I am trying to use your script to phase targeted genes form some samples. I followed your tutorial to generate the different files with GATK then whatshap. However I am not sure to really unde…
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Hi,
I created a test file like this:
```
@test1
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!…