hi, I'm linelle,

Skills

R
Python
Git
Bash
genome assembly
population genomics
GATK
Galaxy platform
selection scans
IGV
PLINK
PacBio HiFi
VCFtools
picard
samtools
Bionano optical maps
Hi-C scaffolding

Education & experience

For more information, have a look at my curriculum vitae .

Papers (orcID)

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

Larivière, D.†, Abueg, L.†, Brajuka, N.†, et al. (2024, Nature Biotechnology) († = first authors)

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genome assembly galaxy platform bioinformatics

Gfastats: conversion, evaluation, and manipulation of genome sequences using assembly graphs

Formenti, G., Abueg, L., Brajuka, A., Brajuka, N., Gallardo, C., Giani, A., Fedrigo, O., and Jarvis, E.D. (2022, Bioinformatics)

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assembly graphs bioinformatics genome assembly

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads

Uliano-Silva, M., Gabriel R. N. Ferreira, J., Krasheninnikova, K., Darwin Tree of Life Consortium, Formenti, G., Abueg, L., Torrance, J., Myers, E. W., Durbin, R., Blaxter, M., and McCarthy S.A. (2022, bioRxiv)

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mitochondrial dna long reads genome assembly

Exome sequencing of deer mice on two California Channel Islands identifies potential adaptation to strongly contrasting ecological conditions.

Orrock, J.L., Abueg, L., Gammie, S., and Munshi-South, J. (2021, Molecular Ecology)

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molecular ecology population genomics selection scans

Presentations (see posters here)

Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data

Video tutorial: Linelle Abueg
Written tutorial: Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Brandon Pickett, Linelle Abueg, Anton Nekrutenko.

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Reproducible & high-quality genome assembly on public computational infrastructure (click link for video)

Linelle Abueg (click link for video!)

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Validation of a near telomere-to-telomere genome assembly for HG002 with Hi-C and ultra-long reads

Brajuka, N., Abueg, L., Fedrigo, O., Jarvis, E.D., Formenti, G., and HPRC-T2T Consortium (2022: Human Pangenome Reference Consortium annual meeting, Bethesda, MD)

Reproducible and high-quality genome assembly and evaluation workflows in Galaxy

Abueg, L., Brajuka, N., Palmada-Flores, M., Gallardo, C., Grüning, B., Larivière, D., Nekrutenko, A., Ostrovsky, A., Schatz, M., Jarvis, E.D., Fedrigo, O., and Formenti, G. (2022: Biology of Genomes, Cold Spring Harbor, NY)

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