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Hi there,
I browsed your interesting [paper](https://doi.org/10.1093/nar/gkad158) (that isnt mentioned in the README) and was intrigued by the speed improvement while promising a similar performanc…
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request from @bebatut
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I'm using geminimulti and pisces on some targeted amplicon sequencing, but each run might contain a different mix of amplicons located around the genome so I can't easily use the chromosomes option to…
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I have a two-part question about small batches where processing 5-6 controls is not financially feasible. Context shall follow.
1. Is the recommendation for 5-6 controls a relatively fixed value or…
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"Latest mapping file downloaded is empty, however AGP mapping files in the past were downloaded with no trouble."
Review download buttons from existing plates, etc. and ensure content is downloadab…
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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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Hi,
Can you add a new filter option using the expected error (sum of (P))?
EE is more useful for amplicon sequencing than the average Q or sliding window method.
Thanks!
Zewei
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I want to use MGcounts's ability to find communities of multimapping features, on some sequencing data of synthetic constructs. I have made a fasta, aligned to it, and made a fake gtf file with all of…
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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…
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[Suggestion to add amplicon resequencing data-processing functionality, brief description of new scripts to aid in this, and request for guidance on unit testing or code review]
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## Justification …