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This is not an issue but just a question: what would be the optimal settings for __fast__ generation of unitigs? I expect running on a SSD or even better a ram drive should help. What about any of the…
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Hi there,
I have a few contigs in my assembly whose header contains a colon. For example:
```transfrag_1:293290599-293291609```
This appears to be causing an error in the ```generate_scaffold…
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Hi,
I've been using COBS in a pipeline I'm working on, but I've noticed what appear to be false negatives in COBS' querying results.
I've used the following script to build compressed COBS and M…
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The print statement:
print("code contains errors : first pass merging was not enough to merge all bins which should be merged ", file=sys.stderr)
in Common_unitigs.py
Is I think not python2.…
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I'm seeing a few duplicate kmers in my output, which would seem to be unintended according to this statement in the github README:
> ... a k-mer and its reverse complement are considered to be the sa…
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This is an enhancement request to add to the bcalm output a list of abundance counts for each kmer in the unitig. This should preserve the equivalent counts in DSK.
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Hi Mikko
I am trying to use GraphAligner for a MHC graph (this is the MHC2 graph in our [paper](https://alurulab.cc.gatech.edu/PaSGAL)- "Accelerating sequence to graph alignment"). However, with bo…
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Cases where a canonical kmer has a canonical neighbour that is itself, will get dropped from the graph currently with the new dbg building algorithm. E.g ATA has a fw AND bw neighbour TAT (canonically…
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Revise implementations of `call_unitigs` and fix the bug
First check `BOSS::call_unitigs`
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Hi,
For me the error is happening while loading the Hi-C data:
`bedfile loaded Starting Iteration 1 python /opt/apps/salsa/SALSA-2.2/fast_scaled_scores.py -d scaffolds -i 1 sort -k 5 -gr scaffol…