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Would it be possible in `compare` or `index` to include a TF-IDF-style step that reweighted the k-mers based on their "rareness" in the corpus? i.e. k-mers that are ubiquitous would receive a lower we…
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Hi!
I'm a computer engineering student and I'm doing my master thesis on improving UST basically (see [here](https://github.com/enricorox/USTAR) if interested).
I wrote a simple C++ program that e…
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# Example
```
@co (((((((R34-3063:0.000399926[&&NHX:dist=0.000399926:kmers_full=2060211:kmers_reduced=59161:path=R34-3063.fa:support=1.0],365152:0.000275801[&&NHX:dist=0.000275801:kmers_full=2…
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I have installed IGGPIPE in Ubuntu 14.04 lts workstation following the guides of IGGPIPE instructions. While running test data, it throws error. Following is the log file:
getSeqInfo file(s) for ge…
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Hi, I found the pangenie-index calculate the unique kmers in the variant flank sequences, so could you please tell me what the unique kmers are used for pangenie genotyping?
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Hi @greg7mdp
You helped me a few months ago implementing parallel joining of maps:
https://github.com/greg7mdp/parallel-hashmap/issues/234
This was working fine, but recently I started having trou…
gf777 updated
5 months ago
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I have a simple/naive thought re reverse-hashing the kmers. We can provide an option to Minhash `reversible = True` to use a reversible hashing function like the Integer Hashing to retrieve back canon…
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Dear Bernardo and Gonzalo,
I am trying use w2rap-contigger as an alternative to discovar denovo for a 2x150bp library (mean fragment size ~350bp stdev: 77bp). The library was sequenced for a 1.2Gb …
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Hi,
Is there a way to extract species-specific kmers from the database and assemble them into species-specific sequences as long as possible?
These can then be used to design diagnostic PCR primers…
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Hello! When I run the code I get the following error and when I check the log file logs/count_kmers/kmc/22558Bue_BER03/kmc_canon.log it is empty. Any help is much appreciated!
[Tue Feb 13 10:07:53 …