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OmicsBox Update Version 1.4

OmicsBox Update Version 1.4

We are happy to announce the latest version of OmicsBox 1.4, a very technical release of the OmicsBox base platform. We upgraded many internal libraries and updated to the latest version of many underlying software packages. These changes required a lot of code-refactoring and software testing to comply with all our internal security and quality standards.

OmicsBox is now more than ever ready to provide a robust and versatile platform for your high-performance scientific data analysis. Additionally, we improved many bioinformatics features throughout OmicsBox to maintain the software and ensure up-to-date database versions. Several parameter options have been adjusted to make complex analysis pipelines as easy as possible. Please find all the details below.

New Features:

Metagenomics Module

  • Taxonomic Classification: Kraken2 database update and new parameters
  • Taxonomic Classification: New option to add, remove and rename samples
  • Taxonomic Classification: Improvements to bar chart

Transcriptomics Module

  • RNA-Seq de novo Assembly: Trinity update (v2.10.0), improved performance and new parameters
  • GSEA for Pairwise DEA: Ranking is now based on p-values instead of the FDR
  • RNA-Seq Alignment: STAR update (v.2.7.5a) and new reference fasta file format (.gz)
  • RNA-Seq Alignment: New parameter to include Read Group (@RG) header and tags in BAM output
  • Create Count Table Transcript-Level: RSEM update (v.1.3.3)

Genome Analysis Module

  • DNA-Seq Polishing: Improved performance due to parallelized analysis
  • DNA-Seq Alignment: New reference fasta file format (.gz)
  • DNA-Seq Alignment: New parameter to include Read Group (@RG) header and tags in BAM output
  • DNA-Seq Assembly (Flye): Flye Update (v.2.8) and support of PacBio HiFi data
  • MLST: Database update and wizard improvements

Functional Analysis

  • BLAST: New feature “Custom DB Cloud Blast” to run blast against own fasta file

General

  • Genome Browser: New reference fasta file format (.gz)

How to update

  • OmicsBox will update automatically. If you are working with OmicsBox v.1.0 or higher you don’t have to do anything to update to the latest version.
  • If you are still using Blast2GO PRO we highly recommend upgrading to OmicsBox. You can download the latest version here.

 Feedback, questions and feature requests are most welcome. Please write to support@biobam.com or log in to your BioBam Account.

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