User profiles for Shilpa Garg

Shilpa Garg

Technical University of Denmark
Verified email at biosustain.dtu.dk
Cited by 5990

[HTML][HTML] Chromosome-scale, haplotype-resolved assembly of human genomes

S Garg, A Fungtammasan, A Carroll, M Chou… - Nature …, 2021 - nature.com
Haplotype-resolved or phased genome assembly provides a complete picture of genomes
and their complex genetic variations. However, current algorithms for phased assembly either …

Variation graph toolkit improves read mapping by representing genetic variation in the reference

…, JM Eizenga, ET Dawson, W Jones, S Garg… - Nature …, 2018 - nature.com
Reference genomes guide our interpretation of DNA sequence data. However, conventional
linear references represent only one version of each locus, ignoring variation in the …

A robust benchmark for detection of germline large deletions and insertions

…, C Alkan, A Soylev, MC Schatz, S Garg… - Nature …, 2020 - nature.com
New technologies and analysis methods are enabling genomic structural variants (SVs) to
be detected with ever-increasing accuracy, resolution and comprehensiveness. To help …

[HTML][HTML] Computational methods for chromosome-scale haplotype reconstruction

S Garg - Genome biology, 2021 - Springer
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid
genomes, and metagenomes provide important insights into genetic variation associated with …

Gaps and complex structurally variant loci in phased genome assemblies

…, A Frankish, RS Fulton, Y Gao, S Garg… - Genome …, 2023 - genome.cshlp.org
There has been tremendous progress in phased genome assembly production by combining
long-read data with parental information or linked-read data. Nevertheless, a typical …

[HTML][HTML] Semi-automated assembly of high-quality diploid human reference genomes

…, M Escalona, O Fedrigo, RS Fulton, LL Fulton, S Garg… - Nature, 2022 - nature.com
The current human reference genome, GRCh38, represents over 20 years of effort to generate
a high-quality assembly, which has benefitted society 1 , 2 . However, it still has many …

Pangenome graphs

…, J Ebler, M Rautiainen, S Garg… - Annual review of …, 2020 - annualreviews.org
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

[HTML][HTML] A draft human pangenome reference

…, JM Eizenga, X Feng, C Fischer, RS Fulton, S Garg… - Nature, 2023 - nature.com
Here the Human Pangenome Reference Consortium presents a first draft of the human
pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of …

WhatsHap: fast and accurate read-based phasing

M Martin, M Patterson, S Garg, SO Fischer, N Pisanti… - BioRxiv, 2016 - biorxiv.org
Read-based phasing allows to reconstruct the haplotype structure of a sample purely from
sequencing reads. While phasing is a required step for answering questions about population …

[HTML][HTML] Periorbital hyperpigmentation: a comprehensive review

R Sarkar, R Ranjan, S Garg, VK Garg… - The Journal of clinical …, 2016 - ncbi.nlm.nih.gov
Periorbital hyperpigmentation is a commonly encountered condition. There is very little scientific
data available on the clinical profile and pathogenesis of periorbital hyperpigmentation. …