Droplet-based high throughput single cell sequencing techniques tremendously advanced our insight into cell-to-cell heterogeneity. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. In consequence, information on splicing and sequence heterogeneity i...
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformat
J. Ultra-deep, long-read nanopore sequencing of mock microbial community standards. Gigascience 8, giz043 (2019). Article PubMed PubMed Central Google Scholar Magi, A., Semeraro, R., Mingrino, A., Giusti, B. & D’Aurizio, R. Nanopore sequencing data analysis: state of the art, ...
UTP11 is an example that illustrates the advantages of our approach to study NMD-sensitive mRNA isoforms using long-read sequencing. The UPT11 gene encodes the human homolog of U3 snoRNA-associated protein 11 that was identified in yeast and is implicated in the nucleolar processing of pre-18S ...
#以guppy碱基识别后生成的统计文件sequencing_summary.txt为输入,指定长度进行对数转换(便于观察分布) NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed # 指定输入文件为fastq格式,指定输出目录fastq-plots(不指定输出目录默认为当前文件夹,会有一堆报告和图片非常混乱),指定最...
We also aimed to mimic a 1-day workflow with 8鈥 24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5...
sequencing_summary.txt记录的信息最为全面,这也是目前Nanopore QC软件玩花样的竞技场! 其中的19列内容如下: filenamefast5文件名 read_id每个fast5文件对应一条read run_id这次run的id号,一个flowcell通常为一个run,所以sequencing_summary中run_id都一致。如果一个flowcell中途停掉再跑,每跑一次会记录新的run ...
The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing. - liyu95/DeepSimulator
Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens. 展开 ...
Ultra-Rapid whole genome nanopore sequencing pipeline a. Base calling and Alignment Software: Guppy v4.2.2 (Commercial software from Oxford Nanopore Technologies) Minimap2 v2.17-r974 b.1. Small Variant Calling Software: PEPPER v0.5 (Docker image - kishwars/pepper_deepvariant:test-v0.5) Margin (...