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Have you considered other algorithms such as Smith-Waterman, Jaro-Winkler, or even the new/improved Levenshtein-Damerau?
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Hi Phil,
I've been getting this set of errors in Lorikeet when using gkl-rs to perform the smith-waterman alignment. It seems that ocassionally the alignment produced by gkl-rs will produce a CIGAR…
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I was thinking about writing functions/macros to help make write documentation and (user) manual easier, and then I found a TODO in [fuzzy.lisp], which was about reverse fuzzy matching. I started to r…
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Hi, when calculating the `partial_raito` between `abcd` and `abd`, it gives:
```
> partial_ratio('abcd','abd')
80.0
```
According to my understranding, the optimal alignment would be:
```
>…
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The work in [_End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman_ 2021](https://www.biorxiv.org/content/10.1101/2021.10.23.465204v1) formed a differentiable alignme…
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This is a non-trivial task but I think might be possible. The GATK makes use of some specially designed C libraries made by intel which greatly improves the performance of the SmithWatermanAligner and…
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If you call `align_it("", "some long sequence", ...)`, there is a memory leak in the C++ code. I worked around it in issue #409 by not calling the method when one of the strings is blank. However, it …
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I noticed that this method uses a read mapper that is typically used to map reads to a reference genome. However, the "genome" in this case is just a small set of tRNA sequences and it therefore seems…
krdav updated
2 years ago
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Hello, I have some problems with some fasta files.
I've uploaded 330 sequences, this is the output:
**Done. Total sequences: 330. Succeeded: 116. Failed: 214**
The problem is the following:
**U…
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Hello all. I am new to kaldi and recently working on a project utilizing part of kaldi functions. One is segment long utterances, and when running align_ctm_ref.py, it seems it will not append cor…