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See https://github.com/Zymo-Research/figaro
This would be primarily for amplicons with a minor overlap; might work best as a simple helper script.
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One issue we should check is whether the primers used in the amplification match the 5' ends of the sequence. PI mentioned that some custom amplicons may not match up
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Before doing runs, I have been filtering out samples in the Viridian dataset based on two criteria: (1) having full-precision collection dates, and (2) having at most 800 Ns (excluding gaps) in the _*…
szhan updated
1 month ago
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```
$ abricate
SYNOPSIS
Find and collate amplicons in assembled contigs
AUTHOR
Torsten Seemann (@torstenseemann)
```
Crap, did I download the wrong code? I was looking for the antibiotic …
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The current technique that the assembled version is using to detect amplicons has two problems:
1. Some lengths are identified as amplicons when they shouldn't be.
2. Some lengths are not identifi…
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Problem with fungal amplicons. Read quality is generally lower for longer amplicons and split_libraries_fastq.py in QIIME doesn't appropriately handle trimming during quality filtering of length poly…
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Hey Martin!
I ntoiced a weird occurrence when running covid-truth-eval on artic assemblies built from simulated read sets, whereby a true SNP in the VCF of the artic assembly is incorrectly being i…
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I would like to use LACA for shorter amplicons (600 bp) from ONT sequencing.
Can you provide the following options in the laca init so that the config file can work with alternative sequence input…
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Is it possible to demux barcodes on both ends of amplicons, and both strands? I suppose one can currently do it in a two-step approach to demux the 5'-end barcode then set up the second round to demux…
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**Current term details**
```
Term name - 16S recovery software
Term ID - MIXS:0000066
Structured comment name - x16s_recover_software
Definition - Tools used for 16S rRNA gene extraction
```
…