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Thanks for developing Strainy!
I'm trying to use amplicon-based Nanopore reads to figure out strain abundances in bacterial samples. The pool has 740 strains and each sample may contain ~10 of them. …
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I am working on a CRISPR data treated by two sgRNAs and sequenced with targeted sequencing. The distance between the two sgRNA is 3000bp which is much longer than amplicon. The targeted area is the w…
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Hi Jody,
I'm interested in analysing TB amplicon sequencing data with TBProfiler and was wondering if it's suitable for that purpose? Have you considered using amplicon data before and do you have…
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Hi,
Is there a way to use Pavian with amplicon sequencing data (e.g. 16S or 18S)?
Best,
Sam
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Hi Felix,
I'm hoping you can help with an issue I'm having with paired end sequencing. I'm sequencing an amplicon that is 350bp long. The first ~300 bases on the forward read match what I expect. Bio…
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Dear all,
I did amplicon sequencing (16S) from woodchip bioreactors that were used to clean water contaminated with pesticides. I am very new to the field and I am still learning how to analyze the d…
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Dear CAMISIM team,
I am starting to try and use CAMISIM for a bunch of projects we have, but wonder if all of them will fit. For instance, is it possible to use CAMISIM for simulating amplicon sequ…
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@k-florek @fanninpm @erinyoung @tives82 @DrB-S
I have been using Cecret for all things SARS-CoV-2 and our research lab just started to work up a NGS methodology for Human Norovirus sequen…
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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…