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With following sequence of events, abci could left with incorrect state, because both `tx1` and `tx2` will be applied?
- consensus connection begin
- begin block
- deliver tx1
- consensus connec…
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Hi,
I'm using MEME and FUBAR in a dataset of 6 species, but I'm most interested only in one. I'm wondering if for that species I should include all the individual's sequences that I have or just a…
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I have generated consensus sequences for different datasets using C3POa. I am trying to do some stats by stablishing a correlation between the number of subreads and the accuracy of the consensus. Wh…
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Hello:
I got an assembly from MeCAT, then removed removed heterozygous redundancy and assembled scaffolds using [redundans](https://github.com/lpryszcz/redundans). Then after filling gap with PBJel…
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### Description of bug
We performed an hybrid assembly using metaspades (ONT + SR), we had really huge coverage. Nonetheless, one of the final we discovered that there were 5 minority SNPs that were …
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Hello,
I have some short-read genomes that were assembled via reference mapping (different references) that I would like to align to each other. I have consensus sequences with masked reference sites…
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Hello,
In my attempts to use ViralConsensus on the command line, I'm having trouble with certain reference fastas. When I provide a reference of 4153 nt, a consensus fasta is outputted properly. W…
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Hi,
I have been trying to generate a consensus sequence using bcftools consensus, but keep failing miserably. The error that i keep getting is:
The fasta sequence does not match the REF allele …
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implement the consensus generation scripts from plot_alignments -> will lead to significant speed up!
(I didn't look at the code for ages, so it might take some time to get this running again)
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Hi,
I am having some trouble using hyperfreq with some samples in which a large percentage of the sequences are hypermutated. I assume it is because of the consensus sequences that they are compared …