Efficient mapping of accurate long reads in minimizer space with mapquik
Genome Research, 2023 DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (e.g., Pacific Biosciences [PacBio] HiFi) to a reference genome, which poses challenges in terms of accuracy and ...
Bariş Ekim +4 more
openaire +4 more sources
Transcriptome Analyses of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed with Transposable Elements [PDF]
, 2019 Background: Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells.
Alberto, Adrian +9 more
core +2 more sources
Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline [PDF]
, 2014 Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling telomere ...
Courtney, Laura +13 more
core +2 more sources
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
Nature Communications, 2016 Read mapping and alignment tools are critical for many applications based on MinION sequencers. Here, the authors present GraphMap, a mapping algorithm designed to analyze nanopore sequencing reads, that progressively refines candidate alignments to ...
Ivan Sović +5 more
doaj +1 more source
RNF: a general framework to evaluate NGS read mappers [PDF]
, 2015 Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect the accuracy of
Boeva, Valentina +2 more
core +5 more sources
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly [PDF]
, 2012 Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly.
Depristo +15 more
core +1 more source
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
BMC Bioinformatics, 2018 Background The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies.
Lauren Coombe +6 more
doaj +1 more source
Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq [PDF]
, 2014 Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes.
Barrick, Jeffrey E. +8 more
core +1 more source
Storage of photonic time-bin qubits for up to 20 ms in a rare-earth doped crystal
npj Quantum Information, 2022 Long-duration quantum memories for photonic qubits are essential components for achieving long-distance quantum networks and repeaters. The mapping of optical states onto coherent spin-waves in rare earth ensembles is a particularly promising approach to
Antonio Ortu +3 more
doaj +1 more source
Disentangled Long-Read De Bruijn Graphs via Optical Maps [PDF]
, 2016 AbstractPacific Biosciences (PacBio), the main third generation sequencing technology can produce scalable, high-throughput, unprecedented sequencing results through long reads with uniform coverage. Although these long reads have been shown to increase the quality of draft genomes in repetitive regions, fundamental computational challenges remain in ...
Alipanahi, Bahar +4 more
openaire +4 more sources