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Hi,
I have a question about potential filtering steps for the decoil output.
I used Decoil on a sample and found 43 ecDNA, which was more than I was expecting. I have also used coral on the same…
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I have a data from 16S/18S/ITS Amplicon Sequencing. Can I use dada2 for analyzing such data? Should I divide them into 16S, 18S and ITS subsets as the reads have different lengths?
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**Submitting author:** @wsmets (Wenke Smets)
**Repository:** https://github.com/LebeerLab/tidytacos
**Branch with paper.md** (empty if default branch): master
**Version:** v0.3.0
**Editor:** @diazrena…
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Dear experts and colleagues,
I am doing 16S amplicon sequencing for the V3-V4 region. I am wondering whether I can directly use "silva_nr99_v138.1_train_set.fa.gz" for taxonomic assignment or if I …
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Hi @RTRichar,
Thank you for developing MetaCurator. I am using MetaCurator to build a reference database on ITS1, and I have a couple of questions.
1. First, I am unsure about the selection of r…
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Good evening,
We had samples from swine oral swabs that were sent to a core facility for sequencing. I am currently working with 16S V3-V4 amplicon sequences using 341F- 805R primers. Sequences w…
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### Description of the bug
Hi,
I had issues running a few samples through viralrecon 2.5 with ivar_variants_to_vcf.py so I decided to run it on the dev branch and it made it past those errors but …
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I am interested in duplex calling using Dorado but have a few questions that I can't find the answers to.
The Dorado readme describes a process to split pod5 files to enable distributed duplex call…
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I'm trying to run your code and I saw the requirement is BLASR 2.0 but on the BLASR github page installing legacy BLASR isn't possible. So I installed the lastest version (BLASR 5.1) but that version …
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Hi @benjjneb,
For my amplicon sequencing analysis usually I use DADA2 stand alone or Qiime2 based DADA2. Recently, I came across LotuS2 (https://lotus2.earlham.ac.uk) bioinformatics pipeline which …