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Hiya!
First of all thanks for a great tool, i have mainly used it to double check my assembly sizes, as the high contents of repetitive regions have made assembly a bit tricky and I need to ensure…
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Hi,
I'm assembling a 3 Gb diploid mammal, but we know it is likely to be quite homozygous. This is confirmed by the k-mer peak, and hifiasm "correctly" identifies the peaks as `[M::ha_pt_gen] peak_…
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Begin to prepare material for publication within the next few months. Use ticket to update needed material.
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## Expected Behavior
I am clustering billions of protein sequences. I already built the database. I was expecting linclust to run fairly quickly, but it seems to get stuck on the initial `kmermatcher…
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$ velvetg output -exp_cov auto
[0.000001] Reading read set file output/Sequences;
[43.817688] 88015946 sequences found
[110.015839] Done
[218.490050] Reading pre-graph file output/PreGraph
[218.4…
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Hi John,
Thanks a lot for implementing the calculation of the optimal kmer count threshold (ska cov).
I tested it using ska 0.3.1 and a paired-end sample (fastq files available here: https://drive…
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It's also possible to define a likelihood for multi-type branching process for age-stratified data ([Kucharski et al, PLOS Comp Biol, 2015](https://journals.plos.org/ploscompbiol/article?id=10.1371/jo…
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Hello,
I am assembling a highly heterozygous plant genome (haploid genome of ~2.6 Gb) from about 42x HiFi coverage (21x per allele).
My priority is to have phased sequences to scaffold later on, so …
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hi ,
Thanks for hifiasm development. Now,I used hifiasm v0.19.5 version to assemble a 18Gb genome, used 23X HiFi data, the RAM of our compute resource is 3Tb. The asm.ec.bin、asm.ovlp.reverse.bin …
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Summary: Running `easy-linclust` on [SRC](http://gwdu111.gwdg.de/~compbiol/plass/2018_08/) got stuck after the first call of `rescorediagonal`. No progress and no printed information for ~12h. Not sur…