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The countfiles produced only contained a set of 55 genes, all of which seem to be tRNA and rRNA genes.
I tried aligning to genome files from GenBank and RefSeq, the results were the same with both al…
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Hi,
we have set up an experiment with a mixture of three strains and we want to check if these strains evolve over time.
We think about using a mapper like bwa or minimap2 before running breseq t…
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Hi Seeman,
I downloaded few plasmids sequences in Genbank full format from NCBI for plasmid annotation and ran the following command:
`prokka ENT2_Contig6_len_41186_circ_NDM-1_Plasmid.fasta --ou…
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We've encountered issues with the reporting of ORF1ab mutations falling in the ORF1b region where the -1 frameshift is not taken into account by SnpEff.
Nextclade uses a different GFF than viralre…
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Goal is to have a structure-mapped version of the variations displayed in [nextstrain](https://nextstrain.org/ncov).
We envision the following required steps:
- parse [json data](https://data.nextst…
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Hello,
I am having a new error when running funannotate update, The workflow seems to run normally but generate an error when reaching the final step in converting to genebank format and collecting…
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**Are you using the latest release?**
1.8.11
**What command did you issue?**
funannotate annotate -i update_results -oannotated --eggnog $emapper_annotations --iprscan iprscan.fasta.xml --cpus 10…
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extracting features
2022-10-01 21:04:05,628 - INFO - Populating features
2022-10-01 21:04:11,385 - INFO - Populating features table and first-order relations: 105792 features
2022-10-01 21:04:11,38…
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### Publication and Data Information
https://academic.oup.com/gigascience/article/8/5/giz036/5484800
### Additional Information
### Checklist
See [New Genome Documentation](https://github.com/…