Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses.
Sign Up to like & getrecommendations! Published in 2021 at "Genomics"
DOI: 10.1016/j.ygeno.2021.03.018
Abstract: Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the… read more here.
Keywords: illumina short; short reads; real reads; nanopore long ... See more keywords
Generation and application of pseudo–long reads for metagenome assembly
Sign Up to like & getrecommendations! Published in 2022 at "GigaScience"
DOI: 10.1093/gigascience/giac044
Abstract: Abstract Background Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and… read more here.
Keywords: long reads; pseudo long; metagenomic assembly; short reads ... See more keywords
Exploring differential exon usage via short- and long-read RNA sequencing strategies
Sign Up to like & getrecommendations! Published in 2022 at "Open Biology"
DOI: 10.1098/rsob.220206
Abstract: Alternative splicing produces various mRNAs, and thereby various protein products, from one gene, impacting a wide range of cellular activities. However, accurate reconstruction and quantification of full-length transcripts using short-reads is limited, due to their… read more here.
Keywords: short reads; exon usage; rna; exon based ... See more keywords
Resolving the full spectrum of human genome variation using Linked-Reads.
Sign Up to like & getrecommendations! Published in 2019 at "Genome research"
DOI: 10.1101/gr.234443.118
Abstract: Large-scale population analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short-read whole-genome sequencing. However, these short-read… read more here.
Keywords: short read; resolving full; short reads; human genome ... See more keywords
A Review on Sequence Alignment Algorithms for Short Reads Based on Next-Generation Sequencing
Sign Up to like & getrecommendations! Published in 2020 at "IEEE Access"
DOI: 10.1109/access.2020.3031159
Abstract: With recent advances in next-generation sequencing (NGS) technology, large volumes of data have been produced in the form of short reads. Sequence assembly involves using initial short reads to produce progressively longer contigs, and then… read more here.
Keywords: generation sequencing; alignment algorithms; next generation; sequence ... See more keywords
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Sign Up to like & getrecommendations! Published in 2017 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1005595
Abstract: The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can… read more here.
Keywords: genome assemblies; short reads; short long; long reads ... See more keywords
Long-read sequencing for reliably calling the mompS allele in Legionella pneumophila sequence-based typing
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Cellular and Infection Microbiology"
DOI: 10.3389/fcimb.2023.1176182
Abstract: Sequence-based typing (SBT) of Legionella pneumophila is a valuable tool in epidemiological studies and outbreak investigations of Legionnaires’ disease. In the L. pneumophila SBT scheme, mompS2 is one of seven genes that determine the sequence… read more here.
Keywords: short read; short reads; pneumophila; sequence ... See more keywords
Advantages of long- and short-reads sequencing for the hybrid investigation of the Mycobacterium tuberculosis genome
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2023.1104456
Abstract: Introduction In the fight to limit the global spread of antibiotic resistance, computational challenges associated with sequencing technology can impact the accuracy of downstream analysis, including drug resistance identification, transmission, and genome resolution. About 10%… read more here.
Keywords: mycobacterium tuberculosis; short reads; coverage; hybr ... See more keywords