7 Result(s)
within
Nae-Chyun Chen
English
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Article
Open AccessMeasuring, visualizing, and diagnosing reference bias with biastools
Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it. Biastools analyzes and categorizes instances of reference bias. It works in various scenarios: when t...
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Article
Improved sequence map** using a complete reference genome and lift-over
Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, th...
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Article
The complete sequence of a human Y chromosome
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, mo...
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Article
Open AccessCharacterization of large-scale genomic differences in the first complete human genome
The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental dup...
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Article
Open AccessImproving variant calling using population data and deep learning
Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of v...
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Article
Open AccessReference flow: reducing reference bias using multiple population genomes
Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other ...
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Article
Open AccessFORGe: prioritizing variants for graph genomes
There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a v...
