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Use Cases, Reviews, Tutorials

Product Tutorial, Quickstarts, New Features, etc.

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. Therefore, unlike traditional short-read methods, IsoSeq provides a more accurate and complete view of gene expression and alternative splicing events. This comprehensive understanding of

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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 important step in the final biological interpretation of experimental results in most omics studies. For non-model species however this often becomes a difficult endeavor 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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Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.

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Cloud Blast and Cloud Units: How to use resources wisely

This article describes how to run CloudBlast wisely. OmicsBox allows you to perform NCBI Blast searches using a cloud system for high-performance computing. This system runs jobs in parallel and autoscales depending on demand. To control usage we use so-called CloudUnits. These units represent computation time (cpu seconds) on the AWS infrastructure. At the moment only Blast and InterProScan consume

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