Algorithms for Molecular Biology : AMB 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.On weighted k-mer dictionaries
Algorithms Mol Biol. 2023 Jun 17;18(1):3. doi: 10.1186/s13015-023-00226-2.ABSTRACTWe consider the problem of representing a set of [Formula: see text]-mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a [Formula: see text]-mer is efficient. The representation is called a weighted dictionary of [Formula: see text]-mers and finds application in numerous tasks in Bioinformatics that usually count [Formula: see text]-mers as a pre-processing step. In fact, [Formula: see text]-mer counting tools produce very large outputs that may result in a severe bottle...
Source: Algorithms for Molecular Biology : AMB - June 16, 2023 Category: Molecular Biology Authors: Giulio Ermanno Pibiri Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
Pangenomic genotyping with the marker array
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/...
Source: Algorithms for Molecular Biology : AMB - May 5, 2023 Category: Molecular Biology Authors: Taher Mun Naga Sai Kavya Vaddadi Ben Langmead Source Type: research
