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<h4>Motivation</h4>In the past decades, many statistical methods for integrating multi-omics data have been developed. They have been implemented into software tools, which differ widely in their programming choices, such as the format required for data …
Read PDF<h4>Motivation</h4>Commercial solutions like 10X cellranger provide robust UMI quantification for their proprietary single-cell protocols, but open methods such as Smart-seq3 lack comparable support.<h4>Results</h4>Here, we introduce umite, a Smart-seq3 UMI counting pipeline with a focus on …
Read PDF<h4>Summary</h4>Sediment DNA-the recovery of genetic material from archaeological sediments-is an exciting new frontier in ancient DNA research, offering the potential to study individuals at a given archaeological site without destructive sampling. In recent years, several …
Read PDF<h4>Summary</h4>Genome-wide association studies have revealed that many disease-associated genetic variants lie in non-coding regions of the genome. To prioritize these variants and clarify their functional roles, accurate classification of <i>cis</i>-regulatory elements is essential. Early approaches …
Read PDF<h4>Motivation</h4>Molecular mimicry is used by pathogens to evade the host immune system and manipulate other host cellular processes. It is often mediated by short motifs in non-homologous proteins, whose detection challenges the sensitivity and specificity …
Read PDF<h4>Summary</h4>In biomedical research, managing computational workflows across numerous projects-with varying parameters, tools, and environments-creates major challenges in scalability, reproducibility, and collaboration. Here, we present WESkit, an implementation of the Global Alliance for Genomics and Health …
Read PDF<h4>Summary</h4>Duplex-Indel is a novel Snakemake workflow for detecting somatic small insertions and deletions (Indels) from Tn5 transposase-based duplex sequencing data. Duplex-Indel enhances the accuracy of mutation calling at the single-molecule level by requiring consensus support …
Read PDFThe Mycobacteria Amplicon Sequencing Tool (https://github.com/guthrielab/MAST) is a modular Nextflow pipeline for antimicrobial resistance prediction and lineage classification of <i>Mycobacterium tuberculosis</i> from amplicon or whole-genome sequencing data sets. The workflow automates read processing, variant calling, …
Read PDF[This corrects the article DOI: 10.1093/nar/lqag029.].
Read PDF<h4>Motivation</h4>The routine exclusion of admixed individuals from traditional genome-wide association studies (GWAS) due to concerns about spurious associations has limited multi-ancestry genetic discovery. Tractor addresses this issue by incorporating local ancestry into association testing, enabling …
Read PDF<h4>Motivation</h4>InterProScan is a widely used software package for large-scale protein function classification and an essential component of UniProt, Ensembl and MGnify Genomes large-scale annotation pipelines. For the past 12 years, InterProScan 5 has provided robust …
Read PDF<h4>Motivation</h4>The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible …
Read PDF<h4>Motivation</h4>In prokaryotic genomes, methylation is an important epigenetic modification that regulates the uptake of foreign DNA; it can also contribute to replication or virulence. We present MPore, a novel method for the database-driven detection of …
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