Comments (1)
Option (2) would probably be faster, as long as your hardware can process that much data. Also, if you are using score calibration (--enable-score-calibration
), you need a minimum of 1,000 per run. I recommend option (2).
If you have sequences with NA
in the coordinates
field of the _virus_summary.tsv
file, it means that geNomad found viral sequences without host segments. It could be: (1) a non-integrated virus, (2) part of a provirus, without a host segment, (3) a provirus with a host segment that was not detected by geNomad.
Detected proviruses will have coordinates in the coordinates
field and geNomad you provide you the sequence with the host regions removed.
from genomad.
Related Issues (20)
- Error downloading database HOT 2
- Inquiry on virus from MAG HOT 4
- [feature request] query database clustering HOT 1
- Whether measures have been taken by genomad to avoid identifying genomic islands as viruses? HOT 5
- AMR annotations on chromsome? HOT 1
- Errors when download and the same issue when running genomad -h HOT 3
- The virus identified by genomad weren't annotated as virus sequence by VIBRANT? HOT 3
- geNomad taxonomy about Baltimore classification HOT 1
- 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
- genomad annotate fastq file is empty or contains multiple entries HOT 3
- 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
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from genomad.