Bioinformatics Advances

This review examines #opensource solutions for managing heterogeneous #bioinformatics data using the data lakehouse paradigm. The authors assess tools for storage, ingestion, and metadata management, define key system requirements, and evaluate alignment with FAIR principles.

🗂️ Just out in Bioinformatics Advances: "Review of open-source software for developing heterogeneous data management systems for bioinformatics applications"  

Explore the full study: https://doi.org/10.1093/bioadv/vbaf168

Authors include: @tuliodna.bsky.social

GitHub - interactivereport/ScaleSC: ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. https://doi.org/10.1093/bioadv/vbaf167 ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. https://doi.org/10.1093/bioadv/vbaf167 - interactivereport/ScaleSC

🖥️ ScaleSC is #opensource and designed for accessibility on single-GPU systems. 

Code and documentation:

ScaleSC is a GPU-accelerated pipeline for single-cell #RNA-seq analysis that supports datasets with up to 20 million cells. Built on Scanpy and Rapids-singlecell, it resolves key CPU/GPU discrepancies, improves scalability, and includes tools for marker identification and cluster merging.

🧠 Just out in Bioinformatics Advances: "ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU"  

Explore the full study: https://doi.org/10.1093/bioadv/vbaf167

GitHub - BioinfoUNIBA/IsoPrimer: A primer-designing pipeline for the amplification of splicing variants A primer-designing pipeline for the amplification of splicing variants - BioinfoUNIBA/IsoPrimer

🛠️ IsoPrimer is freely accessible on GitHub, complete with documentation, example data, and configuration templates to support custom RNA-seq validation workflows:

IsoPrimer automates the design of PCR primer pairs that account for RNA-seq-derived expression of alternative splicing variants. It prioritizes primers based on expression, targets exon–exon junctions, and performs in silico validation to ensure specificity.

🧬 Now published in Bioinformatics Advances: "IsoPrimer: a pipeline for designing isoform-aware primer pairs for comprehensive gene expression quantification" 

Explore the full study: https://doi.org/10.1093/bioadv/vbaf171

GitHub - malikmtahir/LOCO-m6A Contribute to malikmtahir/LOCO-m6A development by creating an account on GitHub.

💻 Access the source code, example datasets, and detailed documentation to apply these models for robust m6A site prediction across genomic regions:

Evaluated with Random-Split and Leave-One-Chromosome-Out strategies, the models outperform existing approaches by improving accuracy and generalizability across chromosomes.

This study introduces two hybrid #deeplearningmodels that combine k-mer composition and one-hot encoded CNN features to predict m6A RNA modification sites.

🧬 Just out in Bioinformatics Advances: "Hybrid representation learning for human m6A modifications with chromosome-level generalizability"  

Full article available: https://doi.org/10.1093/bioadv/vbaf170

GitHub - jlazaroibanezz/citrabounds Contribute to jlazaroibanezz/citrabounds development by creating an account on GitHub.

🛠️ The complete code for the study can be found at

By simulating steady-state fluxes from a kinetic model and translating them as tighter flux bounds, the approach resolves artificial pathway bifurcations between growth and citramalate production in engineered strains.

This work integrates kinetic data into genome-scale constraint-based models of E. coli to produce more realistic flux predictions.

🧪 Now available in Bioinformatics Advances: "Enhancing genome-scale metabolic models with kinetic data: Resolving growth and citramalate production trade-offs in E. coli"  

Explore the full study: https://doi.org/10.1093/bioadv/vbaf166

GitHub - asvarvara/MitSorter: Stand-alone tool for methylation-based discrimination of mitochondrial DNA ONT reads Stand-alone tool for methylation-based discrimination of mitochondrial DNA ONT reads - asvarvara/MitSorter

💻 You can find MitSorter’s source code, documentation, and setup instructions to support precise ONT read classification and reproducible mitochondrial variant analyses here:

It aligns reads to the mitochondrial genome with base modification calls, partitions them by methylation status, and improves accuracy in mtDNA variant calling and downstream analyses.

MitSorter is a command-line tool that separates Oxford Nanopore long reads into mtDNA and NuMT categories by exploiting differences in CpG methylation.

🧫 Recently published in Bioinformatics Advances: "MitSorter: A standalone tool for accurate discrimination of mtDNA and NuMT ONT reads based on differential methylation"  

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf135

GitHub - muellan/rmapalign3n: fast 3N read aligner fast 3N read aligner. Contribute to muellan/rmapalign3n development by creating an account on GitHub.

🖥️ You can access RMapAlign3N along with detailed documentation, example data, and setup instructions to enable reproducible mapping of nucleotide conversion reads:

It combines MinHash-based indexing with multiple sequence alignment filtering, outperforming HISAT-3N, BSMAP, Bismark, and SLAM-DUNK on simulated and real BS-seq and SLAM-seq datasets while scaling efficiently on multi-core CPUs.

RMapAlign3N is a C++ tool for mapping 3N-converted sequencing reads with improved speed and accuracy.

🧬 Now published in Bioinformatics Advances: "RMapAlign3N: Fast Mapping of 3N-Reads" 

Explore the full study: https://doi.org/10.1093/bioadv/vbaf164

GitHub - liviurotiul/PeGAS Contribute to liviurotiul/PeGAS development by creating an account on GitHub.

💻 PeGAS is open source and freely available with documentation, example data, and installation instructions for reproducible bacterial genome analysis:

It offers quality control, assembly assessment, and comprehensive visualization in streamlined, reproducible workflows.

PeGAS is an integrated pipeline for bacterial genome analysis that combines AMR profile prediction, virulence factor detection, plasmid replicon assignment, MLST typing, and pangenome analysis.

🦠 Now available in Bioinformatics Advances: "PeGAS: A Versatile Bioinformatics Pipeline for AMR, Virulence and Pangenome Analysis"  

Full article available:

GitHub - nicokubi/penetrance: An R package for the estimation of age-specific penetrance for complex family-based studies in a format compatible with with the PanelPRO R package. An R package for the estimation of age-specific penetrance for complex family-based studies in a format compatible with with the PanelPRO R package. - nicokubi/penetrance

🧰 The package is #opensource and freely available with documentation, examples, and installation instructions for reproducible penetrance estimation workflows:

It supports flexible prior specification, handles missing age data, and includes options for sex-specific modeling to improve genetic risk assessment in hereditary syndromes.