PBSIM: PacBio reads simulator—toward accurate genome assembly [PDF]
Bioinformatics, 2012 Abstract 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), both of which could be useful for de novo assembly of genomes.
Yukiteru, Ono +2 more
openaire +2 more sources
Improving Genome Assemblies by Sequencing PCR Products with PacBio [PDF]
BioTechniques, 2012 Advances in sequencing technologies have dramatically reduced costs in producing high-quality draft genomes. However, there are still many contigs and possible misassembled regions in those draft genomes. Improving the quality of these genomes requires an efficient and economical means to close gaps and resequence some regions.
Xiaojing Zhang +8 more
openaire +3 more sources
Jabba: hybrid error correction for long sequencing reads using maximal exact matches [PDF]
, 2015 Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged
Audenaert, P. +4 more
core +1 more source
Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept [PDF]
, 2019 Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized ...
Bertrand, Sophie +5 more
core +1 more source
Minimum error correction-based haplotype assembly: considerations for long read data
, 2020 The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome.
de Ridder, Dick +2 more
core +1 more source
Comparative genome analysis of Wolbachia strain wAu [PDF]
, 2014 BACKGROUND: Wolbachia intracellular bacteria can manipulate the reproduction of their arthropod hosts, including inducing sterility between populations known as cytoplasmic incompatibility (CI). Certain strains have been identified that are unable to
Harris, Simon R. +3 more
core +2 more sources
Draft Nuclear Genome Sequence of the Liquid Hydrocarbon-Accumulating Green Microalga Botryococcus braunii Race B (Showa). [PDF]
, 2017 Botryococcus braunii has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of B.
Barry, Kerrie +15 more
core +2 more sources
Complete Genome Sequences of a Clinical Isolate and an Environmental Isolate of Vibrio parahaemolyticus. [PDF]
, 2015 Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We report complete genome sequences for two V. parahaemolyticus strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin, respectively ...
Fischer, Markus +4 more
core +2 more sources
PacBio sequencing output increased through uniform and directional fivefold concatenation [PDF]
Scientific Reports, 2021 AbstractAdvances in sequencing technology have allowed researchers to sequence DNA with greater ease and at decreasing costs. Main developments have focused on either sequencing many short sequences or fewer large sequences. Methods for sequencing mid-sized sequences of 600–5,000 bp are currently less efficient.
Kanwar, Nisha +3 more
openaire +5 more sources
Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans [PDF]
, 2014 We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,
Andolfatto, Peter +5 more
core +3 more sources