Results 51 to 60 of about 1,004,545 (280)
PBHoney: identifying genomic variants via long-read discordance and interrupted mapping [PDF]
BMC Bioinformatics, 2014 As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic diversity and become increasingly relevant in genomic studies. However, the identification of larger genomic variants via DNA sequencing is limited by both the incomplete information provided by ...
English, Adam C +2 more
openaire +2 more sources
High-resolution transcriptome analysis with long-read RNA sequencing.
PLoS ONE, 2014 RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing.
Hyunghoon Cho +5 more
doaj +1 more source
A new hash function and its use in read mapping on genome [PDF]
AUT Journal of Mathematics and Computing, 2020 Mapping reads onto genomes is an indispensable step in sequencing data analysis. A widely used method to speed up mapping is to index a genome by a hash table, in which genomic positions of $k$-mers are stored in the table.
Farzaneh Salari +2 more
doaj +1 more source
Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries [PDF]
, 2011 Background Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements.
Kerstens, H.H.D. +5 more
core +3 more sources
Wochenende — modular and flexible alignment-based shotgun metagenome analysis
BMC Genomics, 2022 Background Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization ...
Ilona Rosenboom +12 more
doaj +1 more source
Accurate long read mapping using enhanced suffix arrays [PDF]
, 2010 With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes.
Dawyndt, Peter +4 more
core +1 more source
Discovery of large genomic inversions using long range information. [PDF]
, 2017 BackgroundAlthough many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem.
Alkan, Can +8 more
core +3 more sources
Stranded Mapping from Long Reads v3 [PDF]
, 2018 This protocol demonstrates how to convert raw long reads produced using a strand-specific sequencing protocol (e.g. ONT's strand-switching protocol) into strand-specific mapped reads. The general ides is to use LAST to identify the adapter orientation relative to the genome, and then use that information to reorient called sequences to create a ...
openaire +1 more source
A long read mapping method for highly repetitive reference sequences [PDF]
, 2020 AbstractAbout 5-10% of the human genome remains inaccessible for functional analysis due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. To enable high-quality resequencing of personal genomes, it is crucial to support end-to-end genome variant discovery using repeat-aware read mapping methods.
Chirag Jain +4 more
openaire +1 more source
Pediatric Blood &Cancer, EarlyView.ABSTRACT Background PIK3CA‐related overgrowth spectrum (PROS) includes several rare overgrowth disorders resulting from somatic gain‐of‐function mutations in PIK3CA. Despite treatment advances, including the recent approval of alpelisib for PROS in the United States, literature detailing the patient experience with PROS is limited.
Vamsi Bollu +8 more
wiley +1 more source