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Good day,
I'm currently working on the assembly of a large mammalian genome. I would like to perform the reference-assisted scaffolding using ragout. However, I cannot run progressive cactus on the g…
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Hi,
Thanks for publishing pufferfish! I was interested in trying it for genome alignment, but when I tried to index GRCh38 it printed out a lot of warnings as if it was interpreting it as a transcr…
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Working through a dataset, I found that most of the resulting alignments only included 100K-200K sequence identifiers from the input dataset even though most of my samples have >1M sequences. Unsure o…
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Hi,
I am using mmseqs2 for the taxonomy assignment using NR database. However, Estimated memory consumption is 2T. Is that normal? Also, my input is already protein. My another question is about th…
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Hello.
MMSeq2 dies after write error, The shell output is below. Anyone knows why this happens?
Thanks,
Torsten
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Create directory tmp
search kelp_database uniref50 res…
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Hi, I'm an undergraduate researcher in UW and I'm quite interested about how to construct the "optimal sequence" for each year based on the historical data "H3N2_HA1_all_years_filtered.fasta", which i…
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Hi,
As mentioned in the manual, "HaploMerger2 is not suitable to work on the assemblies with a scaffold N50 size N50>50Kb; it works better when the scaffold
N50>100Kb; and it works much better wh…
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I noticed that the collaborators are using the somatic VCF files to look for somatic mutations in the HLA genes. These genes are known to be problematic for alignments to the human reference genome si…
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Hi, could you clarify in the documentation which things I can put into `--path`? Like if I have the entire spades package downloaded, do I just run it with `--path spades.py=$(which spades.py)`? For…