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Hello,
I want to use alfpy to count k-mers and calculate the Canberra distance for clustering proteomes of multiple species.
The input is usually >500K protein sequences, so I want to be able to…
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Hello Team,
several questions related to omh and edit distance:
1. For edit distance in the edlib (https://github.com/Martinsos/edlib), there can be global, infix and prefix method (e.g., gaps op…
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Hello,
I am trying to bin my MAGs for my metagenomic samples. I am trying to use Metabat2, but it says that I have 0 bins when there are over 1million contigs in a sample, and many are over 1500 bp. …
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This was first mentioned on Slack by Sorina: https://iqbalgroup.slack.com/archives/C5MANUB17/p1504131606000222
This link shows benchmarking of different hash functions for random and sequential int…
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This is not really an issue, just a suggestion -- hope all is well!
We are finding new ways to use SEEKR by specifying custom alphabets. In these experiments, we are encountering words or k-mers th…
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Dear developer:
Under your suggestion, we want to convert the results of MC to GBWT format, but we are not familiar with the conversion steps.
We encountered some problems in vg index, showing insuf…
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## contam_screen_param
field | value
-- | --
Structured comment name | contam_screen_param
Item (rdfs:label) | contamination screening parameters
Definition | Specific parameters used in …
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Hi,
Just wondering if it is normal for some samples to fail at producing output files such as contigs.fasta with metaspades? Out of 180 samples, 5 of them continue to not produce anything and there…
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Regarding the output format the documentation shows an example with
>SRR10092187.6 66 2:4
but I get
>m64077_200131_143655/2/ccs 0-4:15,5-11:16,12-17:13,18-65:17,66-81:11,82-83:16,84-135:13,136-14…
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Is there a reason that 31 is the largest k-mer size possible? Can I change the krakenuniq-build script to allow for a larger k-mer size?
I am switching to KrakenUniq from Kraken2 where I've previousl…