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06/29/2023
Computing all-vs-all MEMs in grammar-compressed text
We describe a compression-aware method to compute all-vs-all maximal exa...
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08/31/2022
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads
We describe an algorithm to find maximal exact matches (MEMs) among HiFi...
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04/12/2022
Efficient Construction of the BWT for Repetitive Text Using String Compression
We present a new semi-external algorithm that builds the Burrows-Wheeler...
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11/13/2020
A grammar compressor for collections of reads with applications to the construction of the BWT
We describe a grammar for DNA sequencing reads from which we can compute...
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08/06/2019
An Index for Sequencing Reads Based on The Colored de Bruijn Graph
In this article, we show how to transform a colored de Bruijn graph (dBG...
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01/29/2019
Simulating the DNA String Graph in Succinct Space
Converting a set of sequencing reads into a lossless compact data struct...
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05/14/2018