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I was wondering if anyone had the opportunity to test parameters for computing ANI between viral genomes.
I guess that the defaults of fragment length of 3000 and minimal number of fragments of 50 i…
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The reason why I'm asking is because VirFinder, geNomad, VirSorter(2), etc. operate on individual contigs then those results are usually fed into CheckV to determine how complete/contaminated the viru…
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Hi,
I'm trying to simulate metagenome reads (including chimeric reads) using pre-trained model and I succeeded in it but I got fasta file of simulated aligned reads with reads that have no headers.…
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First, a suggestion: It would be very helpful to be able to turn off the screen output. We use fastANI with a single query genome against a long list (thousands) of reference genomes (--refList option…
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HI,
is there a way to call peaks genome-wide instead of the chromosome by chromosome? I guess I could make multiple chrxx_chrxx.txt files, and then concatenate all the calls, but i was hoping there w…
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Hi, I took use of `meryl` to identify individual-specific kmers with `difference` subcommand as below:
`meryl difference paternal.meryl/ maternal.meryl/ output paternal-specific.meryl`
`meryl differ…
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Hi,
I was trying to generate starindex and got the following error:
EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem
I did convert the gff f…
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Q: How many sourmash hashes does it take to classify a genome uniquely?
If the answer is 1, then there is a single hash that identifies this specific genome! :tada:
If the answer is “you cannot…
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We sequenced and assembled the chromosomal level genomes of two Malus crabapple cultivars, 'Flame' and 'Royalty'. How to enable HSE to include and search these two genomes?
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Hi,
is the plug'n play variant of the library available for gencode v44 somewhere or is a manual build the only alternative?
thanks
koen.