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### Description of the bug
Viralrecon has worked perfectly for our SCV2 and some hybrid capture protocols (with the metagenomic side). However, when I ran the pipeline by passing a custom bed file an…
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**User story**
As a developer (Ben) I would like there to be fine-grained batch creation validation for sequencing pipelines.
Currently batch validation for sequencing pipelines lives in a few pla…
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I have assembled few bacterial complete genomes using nanopore long reads via Unicycler bold module followed by multiple rounds of polishing by pilon using Illumina Miseq reads.
While submitting the…
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I came across this workflow, and it's perfect for me, who has little experience with command line scripts. I have the same question with [Adaptor issue](https://github.com/ajlabuc/meCLIP/issues/2#issu…
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Trimmomatic fails for sequencing data generated by the Element Biosciences AVITI instrument if Phred33/64 encoding is not provided (quality score is autodetected for Illumina data).
"Error: Unable…
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I have Illumina novaseq, pair ended reads and I want to trim the non-internal adaptors from both ends. The adaptors I used for library praparation are NEB next adaptors for illumina. So I executed the…
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**Describe the bug**
Hi, I am using platon version 1.7 installed through mamba. As input I am using draft assmblies obtained from bacterial whole genome sequencing (enterobacteria, mainly klebsiella)…
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I ran jellyfish count on ccs reads produced from PacBio HiFi sequencing as follows:
```
jellyfish count -C -m 31 -s 1000 -t 10 -o marten.pb.jf m64047_240219_192555.ccs.fasta
```
And subsequent…
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Using free-text entry for the Sequencing Platform field (instrument_model in the submission.xml file) has generated NCBI processing issues in previous submissions. For example, entering "Illumina HiSe…
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It would be helpful if https://illumina.github.io/interop/summary_table.html (and/or the summary cli help docs) included a description of the columns.
For instance, is `Reads PF` actually `% Pass F…