Metagenomic analysis of two soda lakes, with and without cyanobacterial bloom, with OmicsBox

In this use case, we will use the metagenomics tools included in OmicsBox to analyse the microbial communities in two different soda lakes from Brasil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes have high levels of sodium

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quality check

NGS Preprocessing and Quality Control: How-To with OmicsBox

Functional genomics attempts to describe the functions of genes and proteins by making use of data derived from genomic and transcriptomic experiments. Some bioinformatics tools, like OmicsBox, offers biologists to get from raw NGS data through all steps up to the generation of biological insights for a species without any previous genome resources. The bioinformatic process to perform a de

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How to create analysis workflows

OmicsBox/Blast2GO provides an interface to create, edit and run workflows based on the Common Workflow Language (CWL) specification. This interface allows to describe all analysis steps using the functions and tools offered by Blast2GO and connect them to perform a complete analysis in a single run.  This video shows step-by-step how to create a workflow from scratch, define the input

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new version 5

Release Version 5

Release Date: 13/01/2018) Just in time for the PAG Plant & Animal Genome Conference, we launched Blast2GO 5! This major release brings many new features. Most importantly, Blast2GO is now connected to the powerful BioBam Cloud, an AWS  architecture which gives a big boost to many analysis steps. Details below.  To upgrade from version 4 to 5 you have to

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NCBI GenBank Submission

This video shows how to use the ‘Create NCBI GenBank Genome Submission Files’ tool which allows to generate all files (e.g. the Asn1 (.sqn) file) necessary to submit your annotated sequences to the NCBI database. It allows to combine genomic sequences and functional annotations and creates valid GenBank submission files. Additionally, this video explains how to obtain source files (.gff and .annot files), provides

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New Blast2GO Version 3.3

Major Release Version 4

(Release Date: 13/09/2016) We are very happy to announce the release of Blast2GO 4. This new version contains many new bioinformatic features like Differential Expression Analysis, Gene Finding or Gene Set Enrichment Analysis. Blast2GO will update automatically if activated. Otherwise please download the latest version online from here. Feedback, questions, as well as feature requests, are most welcome. Please write

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Coloured Graphs: How to combine multiple functional GO profiles

The Coloured Graph option is a function in Blast2GO which allows to combine and visualize multiple functional profiles within one GO graph. For each group or profile a different color can be assigned and the resulting GO graph can be filtered and colored accordingly. This video shows how to create a text files to generate a Coloured Graph for three

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How to Set Maximum Memory for Blast2GO

OmicsBox/Blast2GO automatically reserves up to 80% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive swapping and will slow down Blast2GO. Follow this guide to manually change the maximum amount of memory Blast2GO will be allowed to use.

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