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Good luck!
Requirements
```sh
apt install \
libdbi-perl \
libdbd-mysql-perl \
curl \
zip \
build-essential \
zlib1g-dev \
libmodule-build-perl \
git
```
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Hi, I found that the example code in the readme file cannot work:
```
from bend.embedders import NucleotideTransformerEmbedder
# load the embedder with a valid checkpoint name or path
embedder…
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```
#########################################################
Running `funannotate clean` unit testing: minimap2 mediated assembly duplications
Downloading: https://osf.io/8pjbe/download?version=1 …
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Hi,
I tried using `format_database.pl` to format the `repbase` data. I basically concatenated all the references.
`cat RepBase21.01.fasta/*.ref RepBase21.01.fasta/appendix/*.ref > repbase_all.fasta…
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Hi
I tried to run `idba_hybrid` in the following way:
```
$ fq2fa --paired out_mit.fq out_mit.fa
$ idba_hybrid --reference mit.fasta -l out_mit.fa -o `pwd`/idba-mit --num_threads 10 --pre_correction …
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So after trying to write some code interfacing `kmers` with some k-mers parsed using `needletail`, I realized we are storing the k-mers in the opposite order. In `kmers` the leftmost nucleotide is st…
rob-p updated
2 years ago
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I'm interested in developing consensus COI reference sequences for major groups in BOLD:
[BOLD](https://www.boldsystems.org/index.php/TaxBrowser_Home)
I'm guessing I can parse the database infor…
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Thank you for developing this useful tool for data splitting. While using SpanSeq to split a dataset of protein sequences, I've encountered two issues:
1. Typo in sequence type option:
In `span…
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I recently had a discussion with Adam Hospital about making the OPTIMADE standard suitable for biomolecular data.
The most important data to share, that is not standard in Optimade, would be:
- …
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Hi David,
I am trying super-deduper in some very very large datasets (like hundreds of millions reads). The reads have a random barcodes (unique molecule identifiers) in 5' and my goal is to collapse …