Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across
the tree of life imposes fundamental challenges for sequencing, genome assembly, and …
the tree of life imposes fundamental challenges for sequencing, genome assembly, and …
A new view of the fish gut microbiome: advances from next-generation sequencing
The fish gut microbiota contributes to digestion and can affect the nutrition, growth,
reproduction, overall population dynamics and vulnerability of the host fish to disease; …
reproduction, overall population dynamics and vulnerability of the host fish to disease; …
ART: a next-generation sequencing read simulator
ART is a set of simulation tools that generate synthetic next-generation sequencing reads.
This functionality is essential for testing and benchmarking tools for next-generation …
This functionality is essential for testing and benchmarking tools for next-generation …
Removing noise from pyrosequenced amplicons
Background In many environmental genomics applications a homologous region of DNA
from a diverse sample is first amplified by PCR and then sequenced. The next generation …
from a diverse sample is first amplified by PCR and then sequenced. The next generation …
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction
Characterizing the errors generated by common high-throughput sequencing platforms and
telling true genetic variation from technical artefacts are two interdependent steps, essential …
telling true genetic variation from technical artefacts are two interdependent steps, essential …
Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges
SJ Helyar, J Hemmer‐Hansen… - Molecular ecology …, 2011 - Wiley Online Library
Recent improvements in the speed, cost and accuracy of next generation sequencing are
revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are …
revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are …
PBSIM: PacBio reads simulator—toward accurate genome assembly
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) …
reads: long and high error rate and circular consensus sequencing: short and low error rate) …
Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data
The Ion Torrent Personal Genome Machine (PGM) is a new sequencing platform that
substantially differs from other sequencing technologies by measuring pH rather than light to …
substantially differs from other sequencing technologies by measuring pH rather than light to …
A comparison of tools for the simulation of genomic next-generation sequencing data
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 …
validating biological models or for gaining an understanding of specific data sets. Several …
Glacial survival of boreal trees in northern Scandinavia
It is commonly believed that trees were absent in Scandinavia during the last glaciation and
first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 …
first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 …