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Hi, I am trying out Ampligone. It works fast but I got a few questions. I am working with Nanopore reads of 16s rRNA amplicons.
1) If you provide the tool with a single reference, than it determine…
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Hello.
I'm checking the files for download and I see some file with name "refseq207nr_classifierpairA.qza", are this files for use with qiime2? Why are there classifierpairB and C?
What is the c…
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Using various strategies we can determine the expected size of an analytical PCR amplicon based on the parts list. Options for this:
1. Crude, but low user demand: assume mID-derived part lengths a…
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Hi,
I have analysed ITS1 amplicons from fungal samples (leaf endophytes) using kraken2 and the PlusPFP-16 indices provided by Ben Langmead.
These amplicons were trimmed for PCR primer sequences, b…
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### Description of feature
Context in [this Tweet](https://twitter.com/nilshomer/status/1498528699670433795?s=20&t=1uKZpUz-ZkBQKuCobNvyGQ). Used by @peterk87 @fmaguire in [this pre-print](https://www…
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I'm trying to cluster with VSEARCH and assign taxonomy to a set of samples using partial LSU amplicons (in fasta format) PREVIOUSLY extracted from ONT long reads using ITSx. I used the following param…
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**Describe the bug**
When trying to simulate reads with length greater than 400, I get an IndexError: list index out of range error
**To Reproduce**
Steps to reproduce the behavior:
` python gen…
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Options:
- [ ] Only Amplicons vs. semi-Amplicons: with only one primer hybridize due to partial sequences
- [ ] Min and max length of the amplicon
- [ ] Ta and max delta-G
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Hi @avierstr,
first of all thanks for this wonderful code.
I have no problems running on a CentOS system with the same Python installation (v.3.8; all dependencies installed via pip3) but o…
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Working with several different sequencing runs of various qualities I am trying to develop intuition for what reasonable quality filtration parameters are in the function `filterAndTrim`. The relevant…