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
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