Short and long read sequencing
<p>Hybrid Genome Assembly and Annotation of a Pandrug-Resistant <em>Klebsiella pneumoniae</em> Strain Using Nanopore and Illumina Sequencing</p>
... Whole-genome sequencing provides the ideal means for the in-depth study of the mechanisms that promote the emergence, evolution and spread of antimicrobial resis- tance; tracking pathogen populations with ...
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12859_2018_article_2051.pdf
... in long read sequences using com- plementary short reads remains a popular method for increasing the utility of long read sequence, particularly since long read ...
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Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing
... from long-read se- quencing data, we developed a novel computational tool called ...the sequencing experiments, thus automatically producing transition and emission matrices for HMM and allowing the ...
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Short Read Whole Genome Sequencing for Laboratory Based Surveillance of Bordetella pertussis
... whole-genome sequencing (WGS), avoid these issues and provide significant insight into ...of short-read WGS ...numerous long repetitive insertion ...lower-throughput long-read ...
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MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
... generate sequencing data on a huge scale, so as to ana- lyze many samples at a great sequencing depth ...Current long read sequencing technologies, such as pro- vided by Oxford Nanopore ...
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Whole-genome haplotyping approaches and genomic medicine
... inference. Long-read sequencing technologies are enabling longer molecular haplotypes, and decreases in the cost of whole-genome sequencing are enabling the sequencing of ...
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Comparison of long read sequencing technologies in the hybrid assembly of complex bacterial genomes
... single-molecule, long-read sequencing platforms, currently represented by Pacific Biosciences' (PacBio) Single Molecule Real-Time (SMRT) and Oxford Nanopore Technologies' (ONT) MinION sequencers, are ...
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Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing
... including short-read WGS, long-read WGS, long insert WGS (liWGS) and microarrays, each with strengths and ...of short-read WGS to identify clinically relevant ...by ...
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Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes
... of short reads, connects frag- mented protein-coding open reading frames (ORFs), reduces data volume, and enables higher-quality functional gene annotation and better phylogenetic taxonomic assign- ments than do ...
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Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance
... with short and long read WGS enabled an assessment of recombination in the VSA harbouring parts of the E5 ...by short read WGS exhibited moderate SNP frequency and low coverage and thus ...
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Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
... total read counts was positively associated with DNA input amount (Additional file 1: Figure ...total read counts were higher for samples processed with the lower adaptor quantities (Add- itional file 1: ...
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Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing
... ™ sequencing platform was used to collect relevant ...DNA sequencing ap- proach has not been used previously to characterize the microbial consortium of a biogas ...™ sequencing is based on ligation ...
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Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology
... for sequencing DNA (Loman and Watson ...as long as 100 kb (Urban et al. 2015). The ultra-long-read-length sequences generated by MinION have been used for de novo genome assembly and ...
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A high performance computational environment for UHTS studies
... Each read and the reference genome are considered as strings of characters in the computer’s memory; each string is composed by long combinations of four letters (A,C,G,T), which represent the four ...
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Deriving Group A Streptococcus Typing Information from Short Read Whole Genome Sequencing Data
... has long been noted that, in addition to gene emm, some GAS strains may possess up to two additional emm-like genes, also known as mrp and enn, which encode M-like proteins designated Mrp and Enn, respectively (8, ...
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Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data
... bases long [5], assembled into several hundred ...of short reads are difficult to assemble [6]. Assemblers designed for short reads are available [7-9] that utilize the de-Bruijn graph method [10] ...
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SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
... assembling short contiguous regions, to trimming remaining contamination poststitching and creating a final set (or optionally, single pooled file) of sequences in the desired format (FASTA or ...
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Recurrent miscalling of missense variation from short-read genome sequence data
... Synthetic exome sequences for both the mouse genome (mm10) and the human genome (hg37d5) were derived from EnsEMBL BioMart (www.ensembl.org) and con- sisted of the sequences of all exons, including non- coding exons, and ...
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SynthEx: a synthetic normal based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
... We calculated the RRs for each matched tumor–normal pair at each 100-kb non-overlapping bin. For each pair of adjacent bins, we calculated the difference of the read ra- tios (RDs; an abbreviation for ratio ...
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Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.
... other sequencing platforms and for other types of sequen- cing data, such as TCR repertoire, cancer genome or viral variant ...other sequencing data ...the sequencing process that is estimated dur- ...
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