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## Expected Behaviour
Unknown
## Current Behaviour
I am trying to re-create the clustered nr database currently featured on the BLAST site. The cluster step appears to stall after merging the…
cef61 updated
2 months ago
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Hi,
I've been trying to run TALC on some human genome long reads files, and I've been getting an error saying "The de Bruijn Graph is empty" on both the ONT Direct RNA and cDNA sequences. I've also…
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General Coding Tips:
1. Avoid the use of hard-coded numbers. It’s best to define your variables under a reasonable name and use them within the rest of your code so that we can understand where the…
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I noticed that using the Nodegraph method ``n_unique_kmers()`` returns 0 whenever a Nodegraph is saved and then reloaded. Minimum working example:
```python
import khmer
import tempfile
import os
…
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Hi,
I am trying to run jellyfish 1.1.12 for use with Quake.
However, I noticed that my qdump files contain (many) zero counts.
If I compare with the output of a normal k-mer count with jellyfish,…
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Dear GIAB team,
while doing some k-mer counting using the files indexed at [sequence.index.NA12878_Illumina300X_wgs_09252015](https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/NA128…
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It's unclear to me what is the difference betwen `MinimizerQueue` and `ImplicitMinimizerQueue`.
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Currently, several functions exposed in python-land are case sensitive in regards to hashing. For example,
1. get
2. forward_hash
3. consume -- not sure
The result is that python code which deals dir…
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Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…