Comments (3)
That's because it's a FASTQ file. I should add a message explicitly stating that those are not supported.
Can you convert it to FASTA with seqkit fq2fa
? Also, are those short or long reads? geNomad is not designed to work with short sequences such as 150bp reads.
from genomad.
Thank you for the quick response. They are short reads and worked with the nf-core/mag https://nf-co.re/mag/3.0.0 workflow for metagenomes so I was trying to use it as a standalone package. Mostly because they were assembled genomes I believe. So pair-end short reads are a no go with genomad? Do you know of any packages that can do similar with pair-end data?
Thanks
from genomad.
If you ran this pipeline, you should have an assembly (or multiple) for your data. The workflow assembles metagenomes prior to binning.
Regarding doing the analysis directly on reads, it depends on what you want. If you want to evaluate presence of known viruses, you could run something like PHANTA or KMCP. For discovery is new viruses or description of virus genomes, this won't do it, you will need assemblies first.
from genomad.
Related Issues (20)
- Error with geNomad v1.8.0, missing tensorflow.keras HOT 5
- mmseqs2 error HOT 3
- Different protein number from genomad and pyrodigal-gv HOT 2
- Small (reference) data for testing HOT 9
- Error while classifying sequences HOT 6
- Error mmseqs prefilter HOT 4
- plasmid classified as virus? HOT 7
- Optimization Request for Analyzing Large Number of MAGs with geNomad HOT 5
- Fewer viral contigs identified from genomad vs virsorter2 HOT 4
- The question about --disable-nn-classification HOT 1
- Provirus detection in genomad vs checkv HOT 6
- Error mmseqs prefilter HOT 2
- Genetic codes HOT 2
- question about integrase identification during provirus identification HOT 3
- How to export the viral DNA gene sequence? HOT 5
- Number of contigs in the assembly HOT 1
- Chromosome classification result HOT 2
- Discrepancy in Output Counts in Genomad HOT 1
- line 19 in aggregated_classfication.py HOT 2
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from genomad.