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
A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933. [PDF]
, 2014 Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype O157:H7, associated with deadly food-borne outbreaks. Because the publicly available sequence of the EDL933 genome has gaps and >6,000 ambiguous base calls, we ...
Aziz, Ramy K +4 more
core +2 more sources
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
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
SMRT-Cappable-seq reveals complex operon variants in bacteria
Nature Communications, 2018 Fragmentation of transcripts can hide operon complexity in genome-wide transcriptome sequencing. Here the authors sequenced a prokaryotic transcriptome using PacBio and provide insights into operon structure and read-through at termination sites.
Bo Yan +3 more
doaj +1 more source
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
Comparative genomic analysis of Chinese human leptospirosis vaccine strain and circulating isolate
Human Vaccines & Immunotherapeutics, 2020 Leptospira interrogans serogroup Canicola is one of the most important pathogens causing leptospirosis and is used as a vaccine strain of the current Chinese human leptospirosis vaccine. To characterize leptospiral pathogens, L.
Ruipeng Zhang +6 more
doaj +1 more source
SVIM: Structural Variant Identification using Mapped Long Reads
, 2019 Motivation: Structural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity and have been
Heller, D., Vingron, M.
core +1 more source
Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding [PDF]
, 2016 We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish ...
A Bairoch +190 more
core +5 more sources