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For assembly of metagenomic samples with HiFi reads, I ran hifiasm-meta with default parameters. The command line was as follow:
hifiasm_meta -t 32 -o asm hifi_reads.fastq.gz
But the process was e…
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I am not aware if @luizirber has done something like this. But here is an example of the application to deal with some real data.
I tested the two approaches to count the number of unique k-mers in …
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- would a user ever enter a site in the Submission Portal?
- check Site ids agains geolocation values for consistency
- application to projects other than Bioscales
- are plots parts of a site?
- …
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Hi!
Thank you for your great tool. I am trying to do hybrid metagenomic assembly of Illumina and Nanopore data. If I only use the Illumina data it works just fine. For hybrid assembly, however, I …
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Hi,
Sometimes a SPAdes assembly will hang indefinitely at `STAGE == EC Threshold Finding (id: ec_threshold_finder)`, at step `(kmer_coverage_model.cpp : 295) ... iteration 8`.
However, if I…
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[Kaiju](https://www.nature.com/articles/ncomms11257) finds maximum (in-)exact matches on the **protein-level** using the Burrows–Wheeler transform.
**TO DO**
Compare the Kaiju classification to K…
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e.g. Input parameter is set to `--num_splits 12` but only 8 contigs are in the input
```
Error executing process > 'AUTOMETA:PRODIGAL (Annotating mock_metagenome)'
Caused by:
Process `AUTOME…
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- [ ] seqprep
- [ ] trimmomatic
- [ ] evaluate https://github.com/common-workflow-language/workflows/blob/master/tools/trimmomatic-Dockerfile
- [ ] "biopython"
- [ ] hmmer
- [ ] evaluate http…
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Would be nice to have some test data that is not to big to reduce runtime but where we know what the expected result is. Even more important when it comes to the statistical analysis!!
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## Is your feature request related to a problem? Please describe
At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only).
…