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Hi there!
We used Jellyfish and GenomeScope on pair-end NGS data to perform k-mer analysis on a new sequenced species of unknown genome size and unknown ploidy nature.
When I've run Genomescope…
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Hi, I estimated the genome size with HiFi data, the estimated genome size is 328Mb with 1.02% hetorozygosity:
![plot](https://github.com/chhylp123/hifiasm/assets/61004157/2387e38c-6636-4ce0-bdab-ce56…
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Hi again!
Just thinking about the RefSeq versus GenBank question for analysis of a metagenome (containment). Aware that Sourmash may struggle with similar genomes (ie strains) due to a smaller numb…
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I am having some trouble understanding GenomeTester4 version 4.2.16 (stable) functionality, notably with the kmer frequency thresholds. For example, I have two datasets A and B and am interested in km…
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wtdbg2 -x ont -g 1.25g -i test.fq.gz -t 10 -fo wtdbg2test
--
-- total memory 131733680.0 kB
-- available 111429804.0 kB
-- 32 cores
-- Starting program: wtdbg2 -x ont -g 1.25g -i tes…
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Hello, in my project I would like to just calculate the kmer counts for one side of the reads, read_1.fq.gz, for example.
And then afterwards, I would like to compare kmer.dump across samples, I wou…
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Hi~
In the last days, I tried to use kage to genotype my population, but it won't work well, please help me take a look:
'''
kage genotype -i 2/PN2_SNP -r data_tmp/CRR493563 -t 16 --average-cov…
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Hello,
I am trying to differentiate between nucleoside analogous and natural nucleotides based on the difference in electrical charge. But I have a couple of concerns:
1. How does xpore assign …
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... because we ultimately want a map of the molecular evidence of an occurrence of a virus, not a map of the experiments that were performed
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Hi All,
Is it possible to query the bwa index for all locations of a single kmer using prophex?