PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac165
Abstract: SUMMARY Use of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable… read more here.
Keywords: pacrat; pacbio; variant mapping; barcode variant ... See more keywords
Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence
Sign Up to like & getrecommendations! Published in 2022 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.02011-21
Abstract: Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and… read more here.
Keywords: soybean rhizosphere; pacbio; sequencing methods; 16s rrna ... See more keywords
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
Sign Up to like & getrecommendations! Published in 2021 at "BMC Bioinformatics"
DOI: 10.1186/s12859-021-04184-7
Abstract: Background Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods… read more here.
Keywords: structural variations; pacbio; variation; pipeline ... See more keywords
Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
Sign Up to like & getrecommendations! Published in 2021 at "BMC Genomics"
DOI: 10.1186/s12864-021-07971-x
Abstract: Background Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work… read more here.
Keywords: sinensis; pacbio iso; pacbio; iso seq ... See more keywords
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome
Sign Up to like & getrecommendations! Published in 2020 at "Plant Methods"
DOI: 10.1186/s13007-020-00629-x
Abstract: The number of studies using third-generation sequencing utilising Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas. Among them, plant full-length single-molecule transcriptome studies have mostly used PacBio… read more here.
Keywords: pacbio; analysis; rna; pacbio nanopore ... See more keywords