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
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
Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the metagenomics module. New feature include OTU Differential Abundance Testing and several new taxonomy plots: Chao1 Diversity, Rarefaction Curves and PCoA. More details can be found below as well as in the online user manual and Metagenomics Module website. New Taxonomy Statistics and Plots
In this analysis, we will reproduce the study that was carried out by Michaela M. Martis et al. in 2017 (doi: http://doi.org/10.1371/journal.pone.0185182) with OmicsBox. Introduction Ascaridia galli is an intestinal parasite which infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and cause some economic problems. The only available treatments are
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
OmicsBox should be cited as follows: OmicsBox – Bioinformatics Made Easy, BioBam Bioinformatics, March 3, 2019, https://www.biobam.com/omicsbox In case you run functional annotation pipeline on your data (Mapping and Annotation), then the citation is as it used to be, Blast2GO.This is for the Blast2GO methodology: Götz S., Garcia-Gomez JM., Terol J., Williams TD., Nagaraj SH., Nueda MJ., Robles M., Talon
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.
Create a taxonomic mapping file to Make Blast Database within OmicsBox OmicsBox allows creating a custom database to run Blast locally. The blast algorithm will run on the user’s computer against a database that is installed locally.In order to do so, we have to either download a pre-formatted NCBI database (see tutorial) or format our own database (see this tutorial
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