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BACKGROUND: Analysing large-scale mass spectrometry-based complex proteomics datasets often overwhelm desktop computational resources and require manual configuration for analysis. While FragPipe delivers rapid peptide identification across diverse sample preparation and acquisition modes (DDA, DIA, TMT), …
Read PDF<h4>Motivation</h4>De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data …
Read PDF<h4>Background</h4>Understanding the structure and function of microbial genomes is crucial for uncovering their ecological roles, evolutionary trajectories, and potential applications in health, biotechnology, agriculture, food production, and environmental science. However, genome reconstruction and annotation remain …
Read PDFHuman endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Originating from ancestral retroviruses that infected germline cells, HERVs typically follow the canonical proviral structure LTR-gag-pol-env-LTR, where …
Read PDFProtein function is inherently spatial: the same molecule can elicit distinct biological outcomes depending on its localization, interacting partners, and surrounding microenvironment. Spatial proteomics enables systematic <i>in situ</i> characterization of protein localization, abundance, and interactions …
Read PDF<h4>Motivation</h4>Verification of sample sex is an essential quality control step in next-generation sequencing studies, typically assessed from genomic data. Clustering individuals by X chromosome heterozygosity (Xhet) and incorporating relatedness estimates offers a practical first-pass screen …
Read PDF<h4>Summary</h4>Next Generation Sequencing is widely deployed in cholera-endemic regions, yet an end-to-end reproducible pipeline that unifies read QC, filtering, reference mapping, variant calling/annotation, recombination screening, and extraction of parsimony informative sites/variant codons, phylogenetic inference for …
Read PDF<h4>Motivation</h4>Targeted enrichment can offset the bias and depth requirements of random-primed second-strand synthesis in 3'-end RNA-seq by reallocating reads to transcripts of interest. We present PeakPrime, a reproducible Nextflow pipeline that (i) identifies high-coverage 3 …
Read PDF<h4>Motivation</h4>Sequence variability can be extremely high, particularly in bacteria due to the rapid accumulation of mutations linked to their high replication rate and environmental selection pressure, which often favors diversifying selection. For most species, there …
Read PDF<h4>Motivation</h4>Chromatin 3D folding creates numerous DNA interactions, participating in gene expression regulation. Single-cell chromatin-accessibility assays now profile hundreds of thousands of cells, challenging existing methods for mapping cis-regulatory interactions.<h4>Results</h4>We present CIRCE, a fast and scalable …
Read PDFAnalyzing genomic variants in large datasets composed of short-read sequencing data is a process that requires multiple steps and computational tools, which makes it a complicated task that is difficult to reproduce across projects and …
Read PDF<h4>Motivation</h4>Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in information, phylogeneticists need new tools and skills to manipulate …
Read PDFRecent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales. It has been proposed that the use of structural information may offer advantages over sequences …
Read PDFData-independent acquisition (DIA) mass spectrometry is a technique used in proteomics to identify and quantify proteins in complex biological samples. While this comprehensive approach yields more complete and reproducible protein profiles than data-independent acquisition (DDA), …
Read PDFNuclear mitochondrial DNA segments (NuMTs) can contribute to cancer development and disease progression by disrupting protein-coding genes. Furthermore, their presence confounds mitochondrial variant detection, underscoring the critical need for robust NuMT detection. Current methods to …
Read PDF<h4>Summary</h4>The ability to generate high-quality genome assemblies is paramount for understanding global biodiversity. To streamline the quality control of the vast amount of assemblies currently being generated, we developed the Genome Evaluation Pipeline (GEP). Our …
Read PDF<h4>Background</h4>Respiratory Syncytial Virus (RSV) causes significant respiratory infections, particularly in young children and elderly adults. Genetic variations in the fusion (F) protein can reduce the efficacy of vaccination and monoclonal antibody treatments, emphasizing the need …
Read PDF<h4>Motivation</h4>Although high-quality chromosome-scale genome assemblies are feasible, assembling large ones remains complex and resource-intensive. This demands reproducible and automated workflows that not only implement current best practices efficiently but also allow for improvement alongside future …
Read PDFWith the current speed of sequencing, there is a desire for standardized and automated genome assembly and annotation to produce high-quality genomes as input for comparative (pan)genomics. Therefore, we created a convenience pipeline using existing …
Read PDFWorkflow management systems (WMS) are essential for creating and automating multi-step data analyses and ensuring the reproducibility of biological insights. Although numerous WMS solutions exist, few provide deep integration of command-line software with the R …
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