Taher Mun
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View article: Minimizing Reference Bias with an Impute-First Approach
Minimizing Reference Bias with an Impute-First Approach Open
Pangenome indexes reduce reference bias in sequencing data analysis. However, bias can be reduced further by using a personalized reference, e.g. a diploid human reference constructed to match a donor individual’s alleles. We present a nov…
View article: Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis
Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis Open
We introduce the Impute-first alignment framework that reduces reference bias in genomics by integrating genotype imputation with pangenome alignment. Beginning with genotyping and genotype imputation using a portion of the input data, a p…
View article: Pangenomic genotyping with the marker array
Pangenomic genotyping with the marker array Open
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 ma…
View article: LevioSAM: fast lift-over of variant-aware reference alignments
LevioSAM: fast lift-over of variant-aware reference alignments Open
Motivation As more population genetics datasets and population-specific references become available, the task of translating (‘lifting’) read alignments from one reference coordinate system to another is becoming more common. Existing tool…
View article: LevioSAM: Fast lift-over of alternate reference alignments
LevioSAM: Fast lift-over of alternate reference alignments Open
Motivation As more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tool…
View article: Reference flow VCF for pre-built genomes
Reference flow VCF for pre-built genomes Open
Pre-built genomes (in VCF format) for the RandFlow-LD and RandFlow-LD-26 methods in reference flow. The references can be built using the reference flow software (https://github.com/langmead-lab/reference_flow). An archival version of the …
View article: Reference flow VCF for pre-built genomes
Reference flow VCF for pre-built genomes Open
Pre-built genomes (in VCF format) for the RandFlow-LD and RandFlow-LD-26 methods in reference flow. The references can be built using the reference flow software (https://github.com/langmead-lab/reference_flow). An archival version of the …
View article: Raw data for reference flow experiments
Raw data for reference flow experiments Open
Raw results data for the reference flow study. Reference flow used public sequence data, where is specified in the manuscript, to generate the results. The figures shown in the manuscript were plotted using the provided processed data. Ref…
View article: Raw data for reference flow experiments
Raw data for reference flow experiments Open
Raw results data for the reference flow study. Reference flow used public sequence data, where is specified in the manuscript, to generate the results. The figures shown in the manuscript were plotted using the provided processed data. Ref…
View article: Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment Open
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the …
View article: Matching Reads to Many Genomes with the <i>r</i> -Index
Matching Reads to Many Genomes with the <i>r</i> -Index Open
The r-index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a genome in the database or to find seeds for reads that do not. T…
View article: Reducing reference bias using multiple population reference genomes
Reducing reference bias using multiple population reference genomes Open
Most sequencing data analyses start by aligning sequencing reads to a linear reference genome. But failure to account for genetic variation causes reference bias and confounding of results downstream. Other approaches replace the linear re…
View article: Matching reads to many genomes with the $r$-index
Matching reads to many genomes with the $r$-index Open
The $r$-index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a genome in the database or to find seeds for reads that do not.…
View article: Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment Open
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the …