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Hii!!!
I want to use rmats-long from espresso.
I have the following problem.
I cannot run ESPRESSO_C.pl even though I have built Parasail.
Please help.
> perl miniforge3/envs/espresso_en…
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The Smith-Waterman algorithm is essentially a paiwise sequence alignment algorithm typically used in bioinformatics to optimally align two (e.g. DNA) sequences.
The Smith-Waterman algorithm can be s…
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Dear All,
I am trying to better understand the Smith Waterman implementation of minimap2. I am basing my understanding on the published minimap2 paper.
Please correct my understanding in case there…
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Hi, thank you for your package! I found strange behavior when there are repeating units at the beginning of the string:
```r
library(text.alignment)
smith_waterman("a b c d", "a b c d", type = "w…
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Mutect2 (GATK 4.1.0.0) fails occasionally in smith waterman native library as below. stderr is attached. I can also provide core dump if necessary.
[stderr.tar.gz](https://github.com/broadinstitute…
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Hello,
I am glad to post about using the isaac4 aligner.
I am wondering that Isaac aligner --use-smith-waterman smart option.
--use-smith-waterman arg (=smart)
One of the foll…
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The [Smith Waterman algorithm](https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm) is a commonly used metric to compare strings. It would be useful to add it to RapidFuzz.
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I don't know if you're interested, but there's a much easier way of doing Smith-Waterman that involves having an extra row and column at the 0th indexes, whose scores are all zero. You only need a sin…
mmcco updated
9 years ago
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After testing out the striped smith-waterman algorithm on some largish datasets, I'm noticing a failure that is not expected. Below is a small test case replicating this issue (blosum matrix can be f…
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Im trying to reproduce some performance numbers mentioned in HCL paper on AWS F1.
```shell
===>The following messages were generated while performing high-level synthesis for kernel: default_func…