The use of Oxford Nanopore native barcoding for complete genome assembly
Sign Up to like & getrecommendations! Published in 2017 at "GigaScience"
DOI: 10.1093/gigascience/gix001
Abstract: Abstract Background The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using… read more here.
Keywords: short read; native barcoding; read data; genome ... See more keywords
Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages
Sign Up to like & getrecommendations! Published in 2017 at "Microbial Genomics"
DOI: 10.1099/mgen.0.000109
Abstract: [This corrects the article DOI: 10.1099/mgen.0.000064.]. read more here.
Keywords: short read; serotyping coli; coli short; corrigendum silico ... See more keywords
The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome
Sign Up to like & getrecommendations! Published in 2022 at "BMC Genomics"
DOI: 10.1101/2022.01.30.478357
Abstract: Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts.… read more here.
Keywords: effects sequencing; read data; noncoding transcripts; long read ... See more keywords
Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
Sign Up to like & getrecommendations! Published in 2024 at "Genome Research"
DOI: 10.1101/gr.278659.123
Abstract: Mapping transcriptomic variations using either short- or long-read RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, whereas short reads still provide improved coverage… read more here.
Keywords: short read; rna sequencing; long reads; short long ... See more keywords
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short-read data.
Sign Up to like & getrecommendations! Published in 2024 at "Molecular ecology resources"
DOI: 10.1111/1755-0998.13933
Abstract: Highly polymorphic markers, such as microsatellites, are invaluable for the study of natural populations. However, contemporary methods for genotyping highly polymorphic variants have serious drawbacks that impede their efficiency. We created Polly, an R package… read more here.
Keywords: short read; read data; polly package; package genotyping ... See more keywords
Reconstructing cancer karyotypes from short read data: the half empty and half full glass
Sign Up to like & getrecommendations! Published in 2017 at "BMC Bioinformatics"
DOI: 10.1186/s12859-017-1929-9
Abstract: BackgroundDuring cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a highly complex, patient-specific cancer karyotype. Using high-throughput technologies… read more here.
Keywords: short read; read data; half; cancer karyotype ... See more keywords
vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
Sign Up to like & getrecommendations! Published in 2019 at "Human Genomics"
DOI: 10.1186/s40246-019-0194-6
Abstract: BackgroundAccurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), plays a fundamental role in next-generation sequencing (NGS) applications. Existing methods for calling these variants often make simplified assumptions… read more here.
Keywords: short read; hmm; hmm based; based method ... See more keywords