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Seqrepo does not currently provide special support for circular sequences. It should.
The easier implementation is with a boolean that assumes the origin at interbase position 0.
An alternative is…
reece updated
6 months ago
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Hi all,
This isn't a bug report, so apologies if this belongs elsewhere.
I've recently been asked about a task which requires some slightly advanced circular permutation manipulation.
The exi…
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Hey there,
is there a command line functionality to extract circular sequences, i.e. plasmids?
There is a tool called `recycler` [github](https://github.com/Shamir-Lab/Recycler) that is doing exactl…
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Is there a command line functionality to extract circular sequences, i.e. plasmids?
There is a tool called `recycler` that is doing exactly this thing, but it is quite slow.
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Hi Wei,
I wonder would it be possible to add a `--circular` option also to `seqkit subset`?
I am currently using `seqkit subset` to extract the flanking regions of some genes with bed files. Som…
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Hi,
After installing SCARlink without issue, I am facing an issue with the first command of the exemplary data.
I run the command in the scarlink conda env:
scarlink_processing --scrna /path/…
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Hi,
I am comparing circular sequences with random start points. It there a way that I can manually change the start points of the seq tracks without changing the mapping of the other tracks to the s…
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Hi, I am trying to run virsorter2 on my contig sequences. I keep encountering this error in "circular-linear-split". At first, I thought i had duplicate sequence names but I checked and there were non…
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Hello,
I would very much like to use this tool for binning my Flye metagenome assemblies.
However, I ran into the following error:
```
graphmb --assembly Flye/ --outdir GraphMB --depth depths.tx…
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Hi there,
for PT networks of hundreds of thousands to millions of links, `quetzal`'s integrity check functions `integrity_test_sequences()` and `integrity_test_circular_lines()` take an indefinite lo…