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How can I enable plasmid option using unicycler?
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currently these go directly under 'chromosome':
![image](https://user-images.githubusercontent.com/50745/122314724-95b1b100-cecd-11eb-9557-44551c284990.png)
they should be inferred to be under '…
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Hey there, I'm getting this issue:
![image](https://cloud.githubusercontent.com/assets/2730609/15131578/0b57d258-1606-11e6-9939-fb3b62286409.png)
Ideally I would be able to view data that isn't "well…
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### Problem Description
We are currently decontaminating the short reads using `bbduk.sh`. Would it make sense to decontaminate the long reads as well?
### Problem Solution
I've seen certain …
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Hi all, I am trying to use shtab for the first time. I would like to autocomplete a positional argument from a
list. I made a choice function `titleselector` that selects from a list based on a pref…
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The user should be able to input refseqs from the latest NCBI database v82 (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/) to be able to index, use in alignment, and possibly even derive circular feature…
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I've been having problem using gbf files downloaded from NCBI. I would get a KeyError from `tree_methods.py` line 1674. It seems to be linked to the `LOCUS` line. For example, the gbf file I'm using s…
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Many bacteria have circular genomes where there is a gene spanning the origin (usually the annotators try to avoid this by shifting the origin), e.g. ``NC_005213`` from *Nanoarchaeum equitans* (which …
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Description: I propose adding a new function molecular_weight() to the BioSequences package that calculates the average or monoisotopic molecular weight of a protein or nucleic acid sequence. The func…
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Hi, I'd like to use circlator to assembly a mitochondrion genome. I have (PacBio) reads and "linear" contig-level assemblies for a number of samples, as well as a different "reference" chromosome-leve…