TL;DR
The developed Snakemake pipeline covers the entire WES analysis workflow, from initial quality control and pre-processing of raw sequencing data to final variant calling and annotation, and will significantly improve accuracy in identifying clinically relevant genetic variants.
A workflow to minimize the effect of WES capture inconsistencies in single-nucleotide variation (SNV) data is proposed, which leads to a considerable decrease in the batch effect signal, potentially increasing the likelihood of finding true biological signals.
Background Whole-exome sequencing is a widely used technology to identify pathogenic variants in cancer. Although sequencing itself has become increasingly accessible, downstream analysis remains computationally complex, presenting a challenge for many researchers. Existing pipelines lack integrated support for somatic...
Summary Current tools for RNA epitranscriptomic modification and structural feature analysis are often fragmented, focusing on single signal types and struggling with processing efficiency, especially as sequencing data volumes increase and single-cell technologies advance. To address this challenge, we developed Modte...
Whole-exome sequencing (WES) enables the identification of rare germline variants contributing to pediatric diseases. Trio-based sequencing, comparing affected children with their parents, is particularly effective for rare disease genetics. However, WES data analysis requires bioinformatics expertise, varies across in...
This chapter covers quality control, normalization, sparse data handling, and transcript quantification for both bulk and snRNA-seq, along with strategies to address challenges such as multi-mapped reads and batch effects, and examines how artificial intelligence and machine learning techniques can improve data process...
A step-by-step protocol for snpArcher, a Snakemake-based workflow that takes raw sequencing reads and a reference genome as input and produces a filtered, joint-called VCF suitable for downstream population genomic analysis, is presented.
We use cookies to run the site and, with your consent, for analytics and to show ads. See our Cookie Policy.
