A comparison of tools for the simulation of genomic next-generation sequencing data

M Escalona, S Rocha, D Posada - Nature Reviews Genetics, 2016 - nature.com
Computer simulation of genomic data has become increasingly popular for assessing and
validating biological models or for gaining an understanding of specific data sets. Several …

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

ND Olson, SP Lund, RE Colman, JT Foster… - Frontiers in …, 2015 - frontiersin.org
Innovations in sequencing technologies have allowed biologists to make incredible
advances in understanding biological systems. As experience grows, researchers …

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

MR Olm, A Crits-Christoph, K Bouma-Gregson… - Nature …, 2021 - nature.com
Coexisting microbial cells of the same species often exhibit genetic variation that can affect
phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a …

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

M Schubert, S Lindgreen, L Orlando - BMC research notes, 2016 - Springer
Background As high-throughput sequencing platforms produce longer and longer reads,
sequences generated from short inserts, such as those obtained from fossil and degraded …

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

PP Edger, R VanBuren, M Colle, TJ Poorten… - …, 2018 - academic.oup.com
Background Although draft genomes are available for most agronomically important plant
species, the majority are incomplete, highly fragmented, and often riddled with assembly …

Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing

Y Jiang, RKC Yuen, X Jin, M Wang, N Chen… - The American Journal of …, 2013 - cell.com
Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet
the genetic causes remain only partially understood as a result of extensive clinical and …

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

K Yoshida, VJ Schuenemann, LM Cano, M Pais… - elife, 2013 - elifesciences.org
Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the
Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its …

Simulating Illumina metagenomic data with InSilicoSeq

H Gourlé, O Karlsson-Lindsjö, J Hayer… - …, 2019 - academic.oup.com
Motivation The accurate in silico simulation of metagenomic datasets is of great importance
for benchmarking bioinformatics tools as well as for experimental design. Users are …

[HTML][HTML] Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

AD Ewing, KE Houlahan, Y Hu, K Ellrott, C Caloian… - Nature …, 2015 - nature.com
The detection of somatic mutations from cancer genome sequences is key to understanding
the genetic basis of disease progression, patient survival and response to therapy …

PBSIM: PacBio reads simulator—toward accurate genome assembly

Y Ono, K Asai, M Hamada - Bioinformatics, 2013 - academic.oup.com
Motivation: PacBio sequencers produce two types of characteristic reads (continuous long
reads: long and high error rate and circular consensus sequencing: short and low error rate) …