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I aligned two genomes of the same genus (divergence \~5-10%;parameter: -p 80) . I got a very large insertion/deletion (\~ 2M bp, CIGAR: 1974305I1938457D) in an alignment, which is absent in the result…
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Dear RepeatModeler developers,
I have been using RepeatModeler for a while now, and I can get it to run on many organisms / genomes. I have also updated to RepeatModeler 2. One thing that I would …
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Hi,
I'm trying to run the kage index step of kage but I get the following error:
TypeError: __init__() missing 1 required positional argument: 'dtype'
My input VCF is only including SV.
The co…
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Hi Simon,
I am new in the field of prediction of viral sequences. I am basically interested in detecting the number of prophages from bacterial genomes (including MAGs) and tested your VirSorter so…
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I have enjoyed using Clair3 (clair3-arm64) for examining natural variants at the whole-genome level. However, I've recently noticed some irregularities that likely need correction.
Specifically, I …
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Hi,
I would like to assemble the plant mitochondrial genome from the whole genome data. The expected total genome size is 1.7 GB Including chloroplast, mitochondrial and nuclear genome). But the mit…
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Hello Daniel,
Just want to ask whether there are plans for also implement dartminhash (https://arxiv.org/abs/2005.11547), which is very fast for sparse dataset (genomes, metagenomes), and much fast…
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Hello again,
I closed the previous issue I was having as I feel we resolved this - the program ran now after I did a first assembly step to reduce the complexity of a full MGS file of raw data.
No…
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Hi,
I've noticed that Sibeliaz creates a very large number of small files in the "alignment" folder while running. I saw about 1.7 million files generated for 3 genomes (sizes 400, 500 and 1000 Mb…
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Hi NCBI Datasets team,
Today I've tried a couple geolocations with the `--geo-location` flag and have run into the `invalid zip archive` error every time.
My attempt with state level "WA"
`…