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@luizirber, one more thing for today (not intending to distract you), it would be really interesting if you could calculate the species accumulation curve (SAC) for hash sets in clusters of metagenome…
nmb85 updated
3 years ago
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I have created u64 representations of a kmer like this:
```
for kmer in needletail::kmer::Kmers::new(seq, 32 as u8 ) {
let km = Kmer::from(kmer).into_u64();
```
Is there a function to revers…
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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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So the design of BioSequences makes it difficult to implement efficient and correct hashing.
We want efficient hashing, because hashing underlies operations like putting stuff in a `Set` or `Dict`, w…
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Hi,
I have two questions about the usage of PanGenie:
1. The paper of PanGenie says that the constructed graph is a directed acyclic graph. Can PanGenie also be used on non-directed acyclic graph…
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Dear Kraken2 developers,
I'm using your excellent kraken2 software in my metagenomics project and have read through your paper on kraken2. And I am really confused about its database buildi…
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The `tetra-freq` module crashes if there is an `N` nucleotide in the nucleotide sequence.
An example error message is:
> File "/home/ubuntu/.local/lib/python3.6/site-packages/magpurify/modules/t…
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Kallisto seems to detect a large number of non-ACGUT characters when none exist. When I try to create an index using kallisto index, this is part of the output:
[build] warning: replaced 5334758 non…
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Hello
When i use the this command :"python mbcclr --resume
-r nanoflit.fasta -o test_output -e umap -c 613187 -k 5 -t 100" , and the finnal.txt just can find one Bin-1. I am not sure that some…
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I don't know if you're interested, but there's a much easier way of doing Smith-Waterman that involves having an extra row and column at the 0th indexes, whose scores are all zero. You only need a sin…
mmcco updated
9 years ago