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BioBam at LongTREC meeting in Sweden

Our Teammate and PhD student Fabian Jetzinger, part of the LongTREC MSCA doctoral network, recently spent two months in Stockholm to collaborate with the developers of the isONpipeline tools. This pipeline, part of the OmicsBox Transcriptomics module, facilitates reference-free transcriptome reconstruction from Oxford Nanopore or PacBio long-read RNA sequencing data. Learning from their expertise and bringing in his own set

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OmicsBox in SEBiBC First Congress: End-to-end Single Cell Data Analysis Poster

  At BioBam we were thrilled to attend and sponsor the First Congress of Sociedad Española de Bioinformática i Biología Computacional (SEBiBC) in Valencia, a gathering of experts and researchers in bioinformatics and computational biology. Thanks to our colleague Marta Benegas, we had the opportunity to showcase our work advancing single-cell RNA sequencing (scRNA-Seq) analysis this year. Single-cell RNA sequencing

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Genome Completeness Assessment with BUSCO

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

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New Taxonomy Databases in OmicsBox

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

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Combining Transcriptomes with TAMA Merge

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

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Understanding maSigPro Timecourse Results

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.

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OmicsBox 3.3 Release

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

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End-to-End Analysis of Long Reads in OmicsBox

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

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

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

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