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Genome Completeness Assessment with BUSCO

Marta Benegas Coll September 11, 2024

Constructing a high-quality genome assembly is a complex and challenging process. De novo assemblies often suffer from fragmentation, gaps, and various types of assembly errors, which can compromise downstream analyses. Ensuring the completeness and accuracy of these assemblies is essential for robust biological insights. This is where BUSCO (Benchmarking Universal Single-Copy Orthologs) comes into play. BUSCO is a widely used

New Taxonomy Databases in OmicsBox

David Seide August 12, 2024

One of the new additions in OmicsBox 3.3 is the non-NCBI taxonomy databases for Kraken2. With this new feature, we provide users with a broader range of options for taxonomic classification, meeting diverse research needs. Taxonomic Classification with Kraken2 Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to DNA reads. It achieves this by examining the k-mers within

Combining Transcriptomes with TAMA Merge

Fabian Jetzinger August 10, 2024

In analyzing long-read RNA-sequencing data, defining a custom transcriptome by identifying novel isoforms is a complex yet essential task that can have far-reaching consequences for any downstream analyses. As long reads allow researchers to examine isoform diversity in significantly greater detail than short reads, long-read sequencing often reveals a large variety of isoforms not yet present in reference annotations, even

Understanding maSigPro Timecourse Results

Marta Benegas Coll August 8, 2024

Understanding how gene expression changes over time and in response to different conditions is crucial in biological research. On this matter, timecourse differential expression analysis allows researchers to track gene expression at multiple time points, uncovering dynamic patterns that provide insights into complex biological processes such as development, disease progression, and response to treatments.

OmicsBox 3.3 Release

Paula Cubilles August 6, 2024

BioinformaticsWe are excited to announce the release of OmicsBox 3.3, the All-In-One bioinformatics software, designed to simplify your research. This latest version integrates a range of new features and improvements, offering improved usability, advanced functionalities, and expanded database support to meet the diverse needs of the bioinformatics community. With a focus on providing powerful tools and resources, OmicsBox 3.3 brings

End-to-End Analysis of Long Reads in OmicsBox

Fabian Jetzinger July 16, 2024

Long-read sequencing has gained widespread popularity in many areas of biological research due to the many advantages these technologies offer over short reads, as well as the decreasing error rates and costs. Nature Methods named it the method of the year 2022. The field of transcriptomics shows particular interest in long reads, as long-read RNA-sequencing can shed light on the

Cutting-Edge Long-Read Transcriptomics Research Published in Nature Methods

Stefan Götz June 11, 2024

We are pleased to announce the publication of a comprehensive study in Nature Methods: Systematic Assessment of Long-read RNA-seq Methods for Transcript Identification and Quantification. This research provides an in-depth evaluation of multiple long-read RNA sequencing technologies, comparing their effectiveness in transcript identification and quantification.BioBam participation in this research highlights its expertise in long-read sequencing technologies and its commitment to

Single Cell RNA-Seq analysis of Arabidopsis thaliana roots

Marta Benegas Coll May 22, 2024

Single-cell RNA-Seq (scRNA-Seq) analysis has been widely used to investigate animal tissue heterogeneity, principally with human and mouse data. However, this technique is increasingly being used to study plant tissues as well with comparable results. Despite the challenges it faces due to the plant cell wall, researchers have been able to perform single-cell analysis with plant protoplasts, bringing the

Population Structure Analysis with OmicsBox

Enrique Presa April 30, 2024

Population structure analysis is a statistical method used to infer the genetic composition and ancestry proportions of individuals within a population. This type of study allows us to understand genetic variation within and between populations. Building admixture models provides insights into evolutionary processes, migration patterns, and even disease susceptibility. ADMIXTURE, now available in OmicsBox, makes this analysis easier by providing a

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Genome Completeness Assessment with BUSCO

New Taxonomy Databases in OmicsBox

Combining Transcriptomes with TAMA Merge

Understanding maSigPro Timecourse Results

OmicsBox 3.3 Release

End-to-End Analysis of Long Reads in OmicsBox

Cutting-Edge Long-Read Transcriptomics Research Published in Nature Methods

Single Cell RNA-Seq analysis of Arabidopsis thaliana roots

Population Structure Analysis with OmicsBox

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Genome Completeness Assessment with BUSCO

New Taxonomy Databases in OmicsBox

Combining Transcriptomes with TAMA Merge

Understanding maSigPro Timecourse Results

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