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Hi,
I am confused about how I can run the program. I have a fastq file and I want to get frequency for k = 20 just for this fastq file. I tried this,
"./cuCLARK -k 20 -T /home/sabah/Desktop/bit…
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Dear Kraken2 developers,
thanks a lot for this fantastic software! I really appreciated adding the --report-minimizer-data flag (borrowed from KrakenUniq) to latest versions of Kraken2, because bre…
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Hi,
I am trying to use complex command to find the union of bunch of kmer counts. However, some kmers do not show in my final output file. For example, kmer AAC exists in 1280.7257 but is missing i…
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Hello,
Thanks for this amazing tool. I am using fastv in perhaps an unusual way. I'm looking to detect the presence or absence of homologous gene clusters in metagenomic data. I started with ~17 mi…
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Hi Roderick!
I'm developing a k-mer counting Python package for internal usage and I'm using needletail as a backend. While developing it, I noticed that `Kmers` and `CanonicalKmers` are inconsiste…
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I would like to compare kmers from two nucleotide sequence fasta files but at the amino acid level, whereby DNA sequence --> peptide sequence --> kmer comparison at aa level --> extract non-unique kme…
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I found code in io.cpp:cortex_read_kmers that assumes kmers fit into a uint64_t which is only true for k
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In the case where a genome data file is empty or otherwise fails to be parsed correctly by jellyfish into a .Jelly file, the kSNP4 run will fail at a later point, and it is likely to be unclear to the…
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when i ran the quast, i got the ImportError,
here is my code
`quast -o quast_B_cep_out -R reference_genome/BCep_ref.fna -G reference_genome/BCep_ref.gff -l spades_default, spades_kmers_careful, mega…
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I would like to try to use a Reindeer index to locate millions of kmers of interest in a genome.
Instead of transforming the genome in its kmers fasta file, which would be long and use disk space, to…