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Hello,
I am trying to run the pipeline-umi-amplicon on the fastq files generated my minion sequencing. However, I am finding a strange error . Here the command line and error found:
`snakemake -j…
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I just came across the preprint and got curious to try out burst.
I need to assigning the taxonomy for Illumina short-reads (MiSeq, up to ~450bp) from an amplicon sequencing run (COI & 16S). Are t…
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We have an automated system that pulls metadata (collection dates and Ct values) for all samples prior to running artic & ncov-tools. We've recently run into a situation where no samples had metadata …
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Hello,
I'm currently working on data preprocessing from multiple Illumina runs.
The first run was sequencend using a v2 kit, while the other runs used v3, which gives me different amplicon sizes (…
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Hello,
Thank you for this great tool!
I'm working with amplicon sequencing data capturing SMN gene. However, my data demonstrate uneven coverage along the SMN1 gene, which has resulted in question…
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Hello,
Thank you for this excellent tool! It is working very nicely on HiSeq/MiSeq data generated from amplicon sequencing of a non-model organism.
I wonder, after stutter filtering, is there …
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Good afternoon!
These two tools seem similar in some ways, and I would appreciate your feedback how how they differ in approach and intended usage.
>a rare read is erroneous if it has a neighbor…
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I have a multiplex run composed of 20 different barcode libraries with all libraries having the same amplicon fragment (same 1st PCR with all the same primers). The sequencing provider sent me the dem…
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> Taxonomic assignment is the core of targeted metagenomics approaches that aims to assign sequencing reads to their corresponding taxonomy. Sequence similarity searching and machine learning (ML) are…
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Hi,
I am trying to work with Porechop to demultiplex my data. The libraries are a bit complex, and I would really appreciate some help here.
We are doing microbiome work, and our hoping to do 16s…