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I was wondering if there was any upper limit (either computationally or experimentally) in terms of the size of the genome(s) to run olivar on. I'm trying to design a primer set for multiple organisms…
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The current amplicon coverage script devised by @dr-david won't work for all sets of primers and corresponding amplicons. The current logic exploits non-overlapping amplicon regions/positions to ident…
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I suggest using the poreCov pipeline as the backend for SARS-CoV-2 wastewater lineage deconvolution from nanopore long reads. You already added `freyja` ( #274 #270), which is great as the current com…
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Hi team
Could you please let me know if this fasta file (screenshot below) work fine for dada2 pipeline to be used instead of silva 1.38? DO you think that is compatible with `assignTaxonomy()`. T…
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# Possible reasons for duplex reads' quality are low
Hello, thank you for increasing the read quality! We always observe higher read mean quality on duplex than simplex reads, especially simplex pa…
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Hi I've noticed there're problematic sites added for V4 as well. Great work guys!
Just wondering if we can have an additional column for the particular setting (sequencing platforms, amplicon version…
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I am doing 16S rna amplicon based ONT sequencing.
My target region is only of 1kb to 2kb in length.
Per sample reads is around 50K.
Will HEERO give me good error filtered estimates ?
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A user is having an issue when their file paths have spaces in an arguments file. This issue does not exist when there is no arguments file. It would be helpful for GATK to be able to parse shell quot…
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The code in PoolListHandler.get identifies amplicon sequencing pools by process of elimination (i.e., any pool that is is not made up of any kind of known pool plate is treated as an amplicon sequenci…
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Hello again!
I want to process the sequencing data obtained by Croce _et al_ in **"Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs"** with TRUS…