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vsearch conda package #131

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MatthewRalston opened this issue Mar 29, 2024 · 1 comment
Open

vsearch conda package #131

MatthewRalston opened this issue Mar 29, 2024 · 1 comment
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dependencies Pull requests that update a dependency file documentation Improvements or additions to documentation enhancement New feature or request

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@MatthewRalston
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Might suggest the use of conda package [vsearch](https://github.com/torognes/vsearch/) to merge reads into 'contigs' i.e. inserts.

@MatthewRalston MatthewRalston self-assigned this Mar 29, 2024
@MatthewRalston MatthewRalston added documentation Improvements or additions to documentation enhancement New feature or request dependencies Pull requests that update a dependency file labels Mar 29, 2024
@MatthewRalston
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Have been reviewing k-mer literature because of the search algorithm. I think I can write my own smith-waterman alignment variant on search alignment and seeding/match optimizer and heuristic which is based on k-mer indices.

The obvious option is on-disk (index+cache based) matching for k-mers but that seems over engineered, so maybe a much simpler k-mer seed region matching strategy is needed for the aligner.

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dependencies Pull requests that update a dependency file documentation Improvements or additions to documentation enhancement New feature or request
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