first module of the Ouro-Tools pipeline, the raw long-read pre-processing module LongFilterNSplit has a dual function for (1) providing comprehensive quality control metrics of a long-read scRNA-seq experiment and (2) pre-processing of raw long-read sequencing data for the downstream analysis...
Through four decades’ development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing (TGS), as represented by two distinct technical approaches developed independently by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). ...
Pangenome analysis using both tools are executed by default, which can be disabled using the option, --skip_roary and/or --skip_pirate. Quick Start Install Nextflow (>=22.10.1) Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full ...
which can be used in whole-genome sequencing projects to yield better repeat resolution and more contiguous genome assemblies. However, although long-read sequencing technologies can produce genomes with long contiguity, the relatively high error rate of long reads has made it challenging to generate...
Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between st...
High-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the gen
sequencing was 0.8 (Additional file1: Fig. S10). The signal peaks (chr20: 52225000–52225500) in ChIP-seq summed up the H3K27me3 loci in heavy and medium states. Furthermore, we presented the mean methylation bin density of each sequencing read (each DNA molecule in the promoter region)...
Product Tutorial, Quickstarts, New Features, etc. Helpful Features, Tips and Tricks Mini-tutorials for common use-cases and to address frequently asked questions FAQs Reference-free analysis of long-read RNA sequencing for non-model species Read More » OmicsBox in a New Scientific Publicat...
How is the N50 read length calculated? What is the median coverage of the tumor genome?Germline Structural VariantsBefore we dive into structural variant (SV) calling, let's get an idea of how SVs look like in long-read sequencing data. I have prepared a BED file with some "simple" germ...
longreadsum bam -i $INPUT_FILE -o $OUTPUT_DIRECTORY ONT POD5 This section describes how to generate QC reports for ONT POD5 (signal) files and their corresponding basecalled BAM files (data shown is HG002 using ONT R10.4.1 and LSK114 downloaded from the tutorial https://github.com/ep...