Featherweight long read alignment using partitioned reference indexes
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Reports"
DOI: 10.1038/s41598-019-40739-8
Abstract: The advent of Nanopore sequencing has realised portable genomic research and applications. However, state of the art long read aligners and large reference genomes are not compatible with most mobile computing devices due to their… read more here.
Keywords: long read; featherweight long; reference; alignment using ... See more keywords
LAMSA: fast split read alignment with long approximate matches
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw594
Abstract: Motivation: Read length is continuously increasing with the development of novel high-throughput sequencing technologies, which has enormous potentials on cutting-edge genomic studies. However, longer reads could more frequently span the breakpoints of structural variants (SVs)… read more here.
Keywords: split read; approximate matches; split; read alignment ... See more keywords
Strobealign: flexible seed size enables ultra-fast and accurate read alignment
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology"
DOI: 10.1101/2021.06.18.449070
Abstract: Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers, in a novel seeding approach… read more here.
Keywords: strobealign flexible; accurate; flexible seed; read alignment ... See more keywords
GANDAFL: Dataflow Acceleration for Short Read Alignment on NGS Data
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Transactions on Computers"
DOI: 10.1109/tc.2022.3144115
Abstract: DNA read alignment is an integral part of genome study, which has been revolutionised thanks to the growth of Next Generation Sequencing (NGS) technologies. The inherent computational intensity of string matching algorithms such as Smith-Waterman… read more here.
Keywords: short read; ngs data; acceleration; read alignment ... See more keywords
Fast and SNP-aware short read alignment with SALT
Sign Up to like & getrecommendations! Published in 2021 at "BMC Bioinformatics"
DOI: 10.1186/s12859-021-04088-6
Abstract: Background DNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies. The accuracy of sequence alignments directly affects the accuracy of downstream analyses, such as variant calling and quantitative analysis… read more here.
Keywords: reference genome; salt; snp aware; reference ... See more keywords
cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms231911484
Abstract: Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment… read more here.
Keywords: cplot contig; contig plotting; plotting visualization; sequence ... See more keywords