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

Jesus Gutierrez March 23, 2020

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

Comparing taxonomic and functional compositions in metagenomic samples

Jesus Gutierrez March 17, 2020

Any annotation of metagenomic sequences, whether it involves pathways, clusters of orthologous genes, species or any other taxonomic or functional classification can be compared across samples. These analyses are encompassed within the Differential Abundance Analysis, and they require robust statistical approaches to achieve reliable results because metagenomics datasets often show under-sampling and low signal-to-noise ratios. All differential abundance analyses can

De novo genome assembly and annotation of fungus in OmicsBox

Marta Benegas Coll March 13, 2020

This project reproduces the study carried out by Hittalmani S. et al. in 2016 about the S. oryzae fungus, which causes sheath rot of rice. We used OmicsBox for all necessary steps till functional analysis in order to predict pathogenic functions. (Original research paper: https://doi.org/10.1186/s12864-016-2599-0)

Draft genome of a new Verminephrobacter eiseniae strain

Mariana Monteiro March 10, 2020

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Mr. Arun Arumugaperumal Mr. Sayan Paul and Miss Saranya Lathakumari, PhD students Dr. Sudhakar Sivasubramaniam Abstract The earthworm Eisenia fetida has a symbiotic bacteria named Verminephrobacter eiseniae in its nephridia. A new strain of V. eiseniae msu was found out and the genome of the bacteria was found hidden in the genome

Exploring transcriptome completeness in OmicsBox with BUSCO

Carlos Menor February 4, 2020

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. Once the assembly is complete, researchers need to know how good it is or compare the quality of similar assemblies generated by different parameters. There are several ways to characterize the quality of transcriptome assemblies. A good metric of assembly

Hybrid Genome Assembly in OmicsBox with SPAdes

Carlos Menor February 4, 2020

DNA sequencing is the process of determining the nucleic acid sequence in DNA, and it is the technology by which the genome of a species can be characterized. Despite the advent of next-generation sequencing, current DNA sequencing technologies cannot read whole genomes at once, but rather reads small pieces of between 20 and 30.000 bases, depending on the technology used.

How to run Blast of the differential expressed genes?

Mariana Monteiro December 10, 2019

It is possible to run Blast only on the differential expressed genes and not on all the data with OmicsBox. One has to select only those sequences that have differential expressed genes in the OmicsBox project.First, make sure that the name of the sequences in the project match the ones from the differential expression results.

New Genome Analysis Features

Carlos Menor October 25, 2019

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the genome analysis module. New feature includes a new DNA-Seq de novo assembly strategy based on SPAdes.More details can be found below as well as in the online user manual and Genome Analysis Module website. DNA-Seq de Novo Assembly: SPAdes SPAdes (St Petersburg genome

New Transcriptomics Features

Carlos Menor October 25, 2019

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the transcriptomics module. New features include Completeness Assessment and Predict Coding Regions. More details can be found below as well as in the online user manual and Transcriptomics Module website. Completeness Assessment The Completeness Assessment functionality provides quantitative measures for the assessment of transcriptome assembly completeness, based on

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

Comparing taxonomic and functional compositions in metagenomic samples

De novo genome assembly and annotation of fungus in OmicsBox

Draft genome of a new Verminephrobacter eiseniae strain

Exploring transcriptome completeness in OmicsBox with BUSCO

Hybrid Genome Assembly in OmicsBox with SPAdes

How to run Blast of the differential expressed genes?

New Genome Analysis Features

New Transcriptomics Features

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