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Configuration file: db_main.toml
Description: miRDB is an online database for miRNA target prediction and functional annotations.
```toml
[db_mirdb]
source_url = "http://mirdb.org/download/miRDB…
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Hi developer,
I am using SortMeRNA to remove rRNA from my metatranscriptome data, and while I expected most rRNA reads to be depleted. The cleaned reads contain 25,721,937 R1 and 25,721,937 R2 reads…
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I have 200 metagenomes extracted from stream biofilms. I binned contigs to obtain MAGs and I dereplicated MAGs obtained in all samples to obtain a final pool of MAGs. Finally I mapped reads from each …
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In the article, PhenotypeSeeker is described as a tool for bacterial genome analysis. How do you think, could in be used for eukaryotes?
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Hello, I hope you are well!
I'm able to download a specific NCBI Assembly via `bactopia --accession [accession]` -- is there a way to do so with a list of NCBI Assembly accessions (i.e bactopia --…
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### Ask away!
While trying to assist a user to run wf-bacterial-genomes on a Linux Cluster, I installed nextflow. After installation,
i tried wf-bacterial-genomes --help and got an error:
./n…
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Hi my error code is as below:
Traceback (most recent call last):
File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/bin/bakta", line 10, in
sys.exit(main())
File "/data/cephf…
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Currently we have `kmc` as our genome size estimator on TheiaProk suite of workflows. This has shown to be widely inconsistent on ONT data, particularly when very long read sequences are present in th…
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Pick a workflow and (try to) run through it. Fix the issues as you discover them.
- [x] [Galaxy 101](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-10…
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Hello,
I am trying to perform a k-mer analysis using pysser for 6,240 bacterial genomes with binary phenotype. I'm having trouble running fsm-lite. The kmer count is using a lot of RAM and the proces…