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Create an extra detail page per node which present the information about that node in a neat way. It should contain:
* A list of all leaf (templates) sequences.
* A sequence consensus overview of th…
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Hi there,
We want to report an issue with a PanGraph that we generated on a dataset representing 1000 E. coli sequences. We believe that 64 of these sequences are not represented correctly by the P…
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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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Hello,
in `itsxpress` it is possible to cluster using the `--cluster_id` parameter, and if I'm not mistaken, it uses vsearch for this.
However, in the output files, I cannot seem to find the num…
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Hello, I have a question. When I used racon to polish, the genome increased from 50Mb to 67Mb. Is this normal?
The following is my run command:
racon -t 10 45_select.fa 45_select.sam assembly.part-…
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### Ask away!
I am running the wf-amplicon on PCR amplicons covering a complete virus genome (4 overlapping long amplicons per sample, pooled in one barcode) and map the reads to a reference genome o…
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In section 4.4 we have the *abstract* definition of a Spend description, and the following consensus rule:
> Elements of a Spend description MUST be canonical encodings of the types given above.
…
daira updated
5 months ago
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It would be great to have the option to create a consensus sequence from an alignment (perhaps a setting to adjust the cut-off frequency), and have this sequence added to the alignment.
Essentially a…
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Hi Ivan,
I started my first Racon run a few days ago. Around the 48 hour mark, I started to wonder how things were still progressing - I observed the following information in the huge (17 G!)`.log` f…
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Earlier today, I fixed a bug in ViralMSA in which consensus sequences with long stretches of `NNNN...NNNN` sometimes would get truncated (I think when stretch length was greater than ~300), and I inco…