RNA sequencing (RNA-seq) that utilises short-read next-generation sequencing (NGS) or long-read sequencing (such as PacBio and Oxford Nanopore Technologies sequencing) is a powerful tool in understanding transcriptional diversity and regulation during various biological processes, including hematopoiesis2...
combination of the long reads with the accuracy of short read sequencing10. This kind of hybrid assembly approach was shown previously to be effective in reconstructing accurate, contiguous genomes, including plasmids containing AMR genes in (pathogenic) wild-type bacteria10,11,12,13. Although not ...
Finding the right fit: A comprehensive evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome datadoi:10.1101/2021.08.31.458285Jeanette L GehrigDaniel M PortikMark D DriscollRicardo Valladares
Long-read sequencing offers great potential to improve genome assemblies. Read lengths from PacBio platforms (Pacific Biosciences, Menlo Park CA) vary but reach into the tens of kilobases [9]. The base call accuracy of individual reads is about 87% [14] and chimera, i.e. falsely joined seq...
However, it has limitations in accurately assembling large genomes and identifying complex genomic variations, such as structural variations and repetitive sequences, due to the short read length. To overcome these limitations, long-read sequencing technologies, such as Pacific Biosciences (PacBio) and...
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucle...
"Salvaging complete and high-quality genomes of novel microbial species from a meromictic lake using a workflow combining long- and short-read sequencing platforms" \ Installation First, you have to installAnacondaorminiconda3 Second, you have to installsnakemakeand mamba via conda. ...
Compared to sequencing by synthesis (SBS) utilized by traditional short-read sequencers, SBB chemistry gives ~15x lower error rates at any given cycle so that you can achieve near-perfect accuracy in short-read sequencing without having to sequence at unnecessary depths....
在这里,我们使用模拟易出错的牛津纳米孔和高精度Illumina read集,系统地研究序列长度和分类单元类型对微生物和非微生物群落元基因组数据分类精度的影响。 我们发现,一般来说,非微生物群落的分类精度要低得多,即使分类分辨率很低(例如,科而不是属)。 结论 ...
(C) assemble long-read sequencing data with short-read polishing: cDNA data: java -jar RNA-Bloom.jar -long LONG.fastq -sef SHORT.fastq -t THREADS -outdir OUTDIR direct RNA data: java -jar RNA-Bloom.jar -stranded -long LONG.fastq -sef SHORT_FORWARD.fastq -ser SHORT_REVERSE.fastq -t...