HASLR: Fast Hybrid Assembly of Long Reads
Sign Up to like & getrecommendations! Published in 2020 at "iScience"
DOI: 10.1016/j.isci.2020.101389
Abstract: Summary Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies. The larger effective length of their reads has provided a… read more here.
Keywords: haslr fast; hybrid assembly; assembly long; long reads ... See more keywords
Nanopore sequencing and assembly of a human genome with ultra-long reads
Sign Up to like & getrecommendations! Published in 2018 at "Nature Biotechnology"
DOI: 10.1038/nbt.4060
Abstract: We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were… read more here.
Keywords: ultra long; human genome; nanopore sequencing; long reads ... See more keywords
De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Reports"
DOI: 10.1038/s41598-019-55908-y
Abstract: Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes… read more here.
Keywords: minion flowcell; brugia malayi; minion; single minion ... See more keywords
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab022
Abstract: Contigs assembled from the third-generation sequencing long reads are usually more complete than the second-generation short reads. However, the current algorithms still have difficulty in assembling the long reads into the ideal complete and accurate… read more here.
Keywords: similar genome; pipeline; genome assisted; long reads ... See more keywords
MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac195
Abstract: Structural variations (SVs) play important roles in human genetic diversity; deletions and insertions are two common types of SVs that have been proven to be associated with genetic diseases. Hence, accurately detecting and genotyping SVs… read more here.
Keywords: based long; detecting genotyping; mamnet detecting; deletions insertions ... See more keywords
SLHSD: hybrid scaffolding method based on short and long reads.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad169
Abstract: In genome assembly, scaffolding can obtain more complete and continuous scaffolds. Current scaffolding methods usually adopt one type of read to construct a scaffold graph and then orient and order contigs. However, scaffolding with the… read more here.
Keywords: scaffold graph; scaffolding method; slhsd hybrid; long reads ... See more keywords
Evaluating approaches to find exon chains based on long reads
Sign Up to like & getrecommendations! Published in 2018 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbw137
Abstract: Abstract Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly… read more here.
Keywords: generation sequencing; approaches find; long reads; exon chains ... See more keywords
Reconstructing viral haplotypes using long reads
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac089
Abstract: MOTIVATION Most RNA viruses lack strict proofreading during replication. Coupled with a high replication rate, some RNA viruses can form a virus population containing a group of genetically-related but different haplotypes. Characterizing the haplotype composition… read more here.
Keywords: using long; haplotypes using; viral haplotypes; reconstructing viral ... See more keywords
Accurate self-correction of errors in long reads using de Bruijn graphs
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw321
Abstract: Motivation: New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50 000 bp long but with an error rate of at least 15%. Reducing the error rate… read more here.
Keywords: long reads; bruijn graphs; correction; method ... See more keywords
Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw811
Abstract: &NA; Identifying overlaps between error‐prone long reads, specifically those from Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PB), is essential for certain downstream applications, including error correction and de novo assembly. Though akin to the… read more here.
Keywords: state; long reads; innovations challenges; state art ... See more keywords
DENTIST—using long reads for closing assembly gaps at high accuracy
Sign Up to like & getrecommendations! Published in 2022 at "GigaScience"
DOI: 10.1093/gigascience/giab100
Abstract: Abstract Background Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read–based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap-closing methods have been developed, these methods often close an… read more here.
Keywords: closing assembly; accuracy; high accuracy; dentist ... See more keywords