Use Cases, Reviews, Tutorials

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Verminephrobacter eiseniae

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

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Busco OmicsBox Screenshot

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

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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.

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A. galli

Transcriptomic response of A. galli to an anthelmintic drug

Jesus Gutierrez October 24, 2019

In this analysis, we will reproduce a study carried out by Michaela M. Martis et al. in 2017 with OmicsBox. (http://doi.org/10.1371/journal.pone.0185182) Introduction Ascaridia galli is an intestinal parasite that infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and causes economic problems. The only available treatments are the Benzimidazole derivatives,

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Metagenomic analysis of microbial communities with OmicsBox

Jesus Gutierrez October 22, 2019

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

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Acinetobacter baumannii

Transcriptome analysis of Acinetobacter baumannii cells under different conditions

Mariana Monteiro June 11, 2019

OmicsBox Supported Project Researchers: Background and Project Overview: A.baumannii, a nosocomial pathogen, ranks first in the WHO’s list of antibiotic-resistant priority pathogen. The problem of increasing frequency of multi-drug resistance in A. baumannii has been further compounded by tolerance to high concentration of antibiotics due to persister cells. Persister cells are phenotypic variants of normal cells that are formed in

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Lipid transcriptome profiling of indigenous Dunaliella sp. isolate

Mariana Monteiro March 20, 2019

BioBam Bioinformatics S.L. Supported Project. Researchers: Nahid Hosseinzadeh Gharajeh Mohammad Amin Hejazi Mostafa Valizadeh Ebrahim Dorani Background and Project Overview: Dunaliella is a unicellular, halotolerant, biflagellate microalga which is already exploited as a platform in food, feed, aquaculture, biomedical, pharmaceutical, nutraceutical and cosmeceutical industries, specifically due to its high production of β-carotene and fine chemicals. There is a wide range

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Expression quantification and differential expression analysis

Expression quantification and differential expression analysis

Carlos Menor November 20, 2018

One of the most common applications of RNA-seq is to estimate gene and transcript expression. It starts with the alignment or mapping of reads and there are two possible alternatives: mapping to the genome when a reference sequence is available or mapping to the transcriptome (e.g. de novo assembled transcriptome). Reads may map uniquely or could be multi-mapped reads, while

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