BamSnap: a lightweight viewer for sequencing reads in BAM files
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa1101
Abstract: SUMMARY Despite the improvement in variant detection algorithms, visual inspection of the read-level data remains an essential step for accurate identification of variants in genome analysis. We developed BamSnap, an efficient BAM file viewer utilizing… read more here.
Keywords: viewer; viewer sequencing; reads bam; lightweight viewer ... See more keywords
QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac313
Abstract: MOTIVATION The existence of quasispecies in the viral population causes difficulties for disease prevention and treatment. High-throughput sequencing provides opportunity to determine rare quasispecies and long sequencing reads covering full genomes reduce quasispecies determination to… read more here.
Keywords: sequencing reads; long sequencing; accuracy; reads quasiseq ... See more keywords
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1101/2022.01.21.477194
Abstract: Summary Viral sequence data from clinical samples frequently contain human contamination, which must be removed prior to sharing for legal and ethical reasons. To enable host read removal for SARS-CoV-2 sequencing data on low-specification laptops,… read more here.
Keywords: sequencing reads; cov sequencing; readitandkeep rapid; rapid decontamination ... See more keywords
New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads
Sign Up to like & getrecommendations! Published in 2022 at "Life Science Alliance"
DOI: 10.1101/2022.08.30.505891
Abstract: Innovative algorithmic approaches were used to perform assembly of complex genomes across the tree of life, from long DNA sequencing data. Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA… read more here.
Keywords: new algorithms; sequencing reads; algorithms accurate; long dna ... See more keywords
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
Sign Up to like & getrecommendations! Published in 2017 at "Genome research"
DOI: 10.1101/gr.211748.116
Abstract: We are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis.… read more here.
Keywords: bwt; sequencing reads; reference; human genomes ... See more keywords
Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms
Sign Up to like & getrecommendations! Published in 2019 at "BMC Genomics"
DOI: 10.1186/s12864-019-6189-9
Abstract: BackgroundWhole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available.… read more here.
Keywords: chromosome isoforms; single sequencing; sequencing reads; chromosomes single ... See more keywords
VGEA: an RNA viral assembly toolkit
Sign Up to like & getrecommendations! Published in 2021 at "PeerJ"
DOI: 10.7717/peerj.12129
Abstract: Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology,… read more here.
Keywords: quality; sequencing reads; reference; vgea ... See more keywords