In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. 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 show high levels of sodium
The Multilocus Sequence Typing Analysis Tool of OmicsBox (MLST) is a nucleotide sequence-based approach of characterizing isolates of bacterial species using the sequences of internal fragments of seven housekeeping genes. This video shows step-by-step how to analyze bacterial sequences with the MLST App in OmicsBox. As input, users can provide either DNA-Seq reads in FASTQ or contigs/scaffolds in FASTA format.
This 5-minute video provides a brief introduction to OmicsBox. All main features of all modules are introduced. OmicsBox is a bioinformatics Solution to easy your Omcis Data Analysis. Our workflows get you from raw reads tp insights fast and easy. The presented modules include Transcriptomics, Functional Annotation and Analysis with Blast2GO, the Genome Analysis Module as well as the Metagenomics
(Release Date: 02/08/2018) We are happy to announce that Blast2GO 5.2 has now been released. This update makes our bioinformatics tool for straightforward functional genomics even better.Read below to learn which features and improvements are part of this release. Main features: Venn Diagrams that are fully customizable and allows multiple list comparisons FastQ Pre-Processing (Adapters, Quality, Length) with multiple trimming options.
This project reproduces a study carried out by Hittalmani S. et al. in 2016 about the S. oryzae fungus which causes sheath rot of rice. We used Blast2GO for the main analysis steps like the structural and functional annotation and analysis. (Original research paper: https://doi.org/10.1186/s12864-016-2599-0) 1. Introduction Sheath rot disease caused by S. oryzae is an emerging threat to rice
The “Create Count Table” feature of OmicsBox/Blast2GO allows quantifying the gene expression of RNA-seq datasets. This video shows step-by-step how to create a count table of raw reads and explains in detail different concepts of expression quantification. The available parameters are inspired by the popular HTSeq Python Package (reference below).
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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