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### **Description**
**Sub-lineage of:** KP.3.1.4
**Earliest sequence:** 2024-6-26, USA, North Carolina — EPI_ISL_19216826
**Most recent sequence:** 2024-7-14, Canada, New Brunswick — EPI_ISL_192840…
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XDY.1 > S:T572I (C23277T)
Query: C23277T,G25082A, G28380A
Samples: 11
Places: 6 including South Africa and Greece
Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace…
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Hello,
I am currently facing an issue with extremely high memory usage while building a Kraken2 database with around 400GB of genomes. When using a 31-mer size, the database construction seems to r…
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I analyzed the intact seq extracted by LTR_retriever with the command 'TEsorter acau.intact.fa -db rexdb-plant -p 36 -rule 70-30-80'. After splitting the sequence into 72 pieces and translating it, an…
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I have two nucleotide sequences: The query is an ORF, the target is a truncated genome sequence, containing an homologous ORF with a high identity to the query.
Despite the high similarity, `mmseqs…
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Hi,
I finally managed to get ufcg running with `--set NUC`, only to realise that it then only uses ITS.
Why isn't it using all the `core` genes in `NUC` mode as it does in `PRO` mode?
Can that …
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When using CIRIquant, we are recommended to use CircAtlas to obtain files like GTF files, reference genomes and whatnot.
Are the sequences of circRNAs present in CircAtlas total or partial?
How is …
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Are k-mers with ambiguous nucleotides (e.g. N) included in the sketch or are they thrown out?
I would imagine the best strategy is to have Mash filter these kmers out. I suppose it could be handle…
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I am not sure to understand the meaning of this statement in the IBIS technical details.
>**3 Baseline Solutions**
>
>During the Leaderboard stage, the baseline for evaluating PWMs and AAAs …
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Hello,
Thanks for developing such great tools!
I am wondering if there is a way to apply tcr-dist on cdr3 amino acid sequences.
Currently, the instructions say it is required "nucleotide sequ…