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code in #40 could benefit from making `SeqToHashes` less opaque over in sourmash.
Some ideas:
* simple and lightweight: provide access to `kmer_index` per https://github.com/oxli-bio/oxli/pull/4…
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Good afternoon,
I am assembling fish genomes de novo using hifi data and have run into a few issues for a few of my target species (all diploid);
first, to better understand the size and heterozyg…
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张老师好! 我组装了一个2倍体基因组, 因为做kmer分析的时候, 整个基因组的杂合度很高, 所以选择装出两套单倍型基因组,我想用subphaser来对这两套单倍型基因组进行分型, -f 参数默认是2,如果我使用-f 默认参数就显示ValueError: 0 kmer remained after filtering. Please reset the filter options. 后来我将-f…
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The following functionality needs to be added:
- [ ] Standardize naming scheme and file form for resistance kmer "db" file
- [ ] New section to configuration file for resistance kmer file
- [ ] U…
ar0ch updated
4 years ago
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Hi, @EricR86 @mehrankr
Thanks for providing an excellent program for calculating genome mappability. I'd like to inquire about a few questions I've had while running umap here.
1. I'm using the…
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Hi,
I have issue similar to #388 #49 #563 , but different in one point.
Namely, I am working with diploid plant genome. I have several individuals sequenced with Pacbio hifi. When assembled with hif…
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Hi,
I am trying to use the SubPhaser to phase the subgenomes of my species. However, after filtering differential kmers, no differential kmers were remained. I used parameter of this `-k 15 -q 50 -…
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Hi Jue and Heng,
Would be able to answer this question: https://bioinformatics.stackexchange.com/questions/7029/wtdbg2-practical-implications-of-k-mer-fsize-and-psize-choice
Thanks!
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Using the glistmaker, I managed to create a .list file using a fasta file for the HG38 reference genome. While I am able to make .db files using this .list file, and while said .db files say they are …
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Hi,
It suggests that flappie has separate models (r941_native and r941mC_native) for R9.4 MinION and PromethION flow cell. Can you please let me know if there is a way to extract the kmer model fro…