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metatranscriptomics SortMeRNA OmicsBox rRNA ribosomal removal filtering

rRNA Removal with SortMeRNA in OmicsBox

Introduction RNA-seq data from metatranscriptomics NGS projects contains both coding and non-coding types of RNAs. Before any gene expression or taxonomic analysis, it is important to separate reads in families of messenger RNAs and ribosomal RNAs (rRNAs). SortMeRNA, first released in 2012, is a fast and accurate tool for filtering ribosomal RNAs in metatranscriptomics datasets. The core algorithm is based

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Contaminant Removal with Bowtie2 in OmicsBox

Metagenomics Contaminant Removal with Bowtie

Introduction A common preprocessing step in metagenomics data analysis e.g. working with host-associated studies is to remove the host-related DNA from the sequencing data. This is often referred to as contamination removal. A common approach to isolate host-related reads is performing a read mapping against the host genome. Bowtie2 is the reference tool for this task. Since OmicsBox 2.0 this

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IsoSeq long-read analysis

IsoSeq De-Novo Isoform Discovery with OmicsBox

Introduction The IsoSeq sequencing method produces full-length transcripts using Single Molecule, Real-Time (SMRT) Sequencing. Long read lengths allow sequencing of full-length transcripts up to 10 kb or longer, removing the need for transcript assembly or inferencing. The IsoSeq bioinformatics pipeline processes the data into high-quality consensus transcript sequences that enable accurate isoform annotation and open reading frame prediction. OmicsBox implements

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Gene Prediction Augustus OmicsBox

Eukaryotic Gene Finding with OmicsBox

Introduction Given a new genome, one of the first and most important tasks is determining the structure of its protein-coding genes. Ab initio gene prediction algorithms play a critical role because they produce gene structures quickly, inexpensively, and remarkably reliable. In OmicsBox, the Eukaryotic Gene Finding application is based on AUGUSTUS, which is one of the most accurate programs for

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Single Cell Clustering Seurat

Single Cell Clustering With Seurat in OmicsBox

Introduction Single-cell RNA sequencing (scRNA-seq) is a technology that aims to study the expression profiles of individual cells, in contrast with the typical bulk RNA sequencing that analyses the expression of large populations of cells together. scRNA-seq allows the identification of different cell types within the same sample, so it is possible to study tissues with more detail. One of

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Combined Pathway Analysis with OmicsBox

Introduction A pathway analysis is an import step in the final biological interpretation of experimental results in most omics studies. For non-model species however this often becomes a difficult endeavour due to the lack of functional information. The Combined Pathway Analysis tool allows to identify pathways from multiple pathway databases for any set of sequences. In combination with differential expression

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OmicsBox Update Version 2.0

BioBam announced today the release of OmicsBox 2.0. This new version of BioBam’s bioinformatics solution offers a user-friendly data analysis platform which allows to get from next generation sequencing reads to biological insights with ease. The software offers “out-of-the-box” data analysis and functional interpretation of genome, transcriptome and metagenome datasets for industry, academic and governmental research biologists. OmicsBox is used

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New OmicsBox Login Dialog

With OmicsBox version 2.0 we introduce a new login dialog. This login is required for a more advanced subscription usage management. The login credentials are identical with the ones used for the BioBam Account website. If you do not yet have an BioBam Account you can easily create one from within OmicsBox via “SIGN UP”. If you forgot your password

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