One of the new additions in OmicsBox 3.3 is the non-NCBI taxonomy databases for Kraken2. With this new feature, we provide users with a broader range of options for taxonomic classification, meeting diverse research needs. Taxonomic Classification with Kraken2 Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to DNA reads. It achieves this by examining the k-mers within
Barcoding and demultiplexing in high-throughput sequencing experiments Barcoding, or indexing, is a widely used strategy in high-throughput sequencing experiments. This method enables the multiplexing of numerous samples in a single sequencing run by adding a unique DNA sequence to each sample before sequencing. During sequencing, the barcodes are read along with the DNA fragments, allowing the identification and split of
On Ubuntu Linux and other distributions, OmicsBox might not start. This can happen due to an incompatibility of JavaFX in combination with Wayland and GTK3. This blog describes a possible workaround for this problem. Step 1: Open a terminal window and check if the following command gives you “wayland”. If it gives you “x11” the OmicsBox is probably not starting
OmicsBox enables users to rename all selected sequences by modifying the existing sequence name through conversion, replacement, or adding text.
Transcriptome sequencing (RNA-Seq) produces big amounts of valuable information on all transcribed elements in the genome. With RNA-Seq, researchers can interrogate the transcriptome to profile gene expression, uncover alternative splicing, and identify novel and discard aberrant transcripts and coding variants, among others. The resulting BAM Files are the source of information for all proceeding step
Introduction RNA-seq data from metatranscriptomics NGS projects contains both coding and non-coding types of RNAs. Before any gene expression or taxonomic analysis, it is important to separate reads in families of messenger RNAs and ribosomal RNAs (rRNAs). SortMeRNA, first released in 2012, is a fast and accurate tool for filtering ribosomal RNAs in metatranscriptomics datasets. The core algorithm is based
Introduction A common preprocessing step in metagenomics data analysis e.g. working with host-associated studies is to remove the host-related DNA from the sequencing data. This is often referred to as contamination removal. A common approach to isolate host-related reads is performing a read mapping against the host genome. Bowtie2 is the reference tool for this task. Since OmicsBox 2.0 this
Activate development on Blast2GO was discontinued in 2018. All its functionality and more new features are now part of OmicsBox. Because Blast2GO is no longer updated, some of its functions may have stopped working because web services have changed or security certificates have expired, among other things. It is highly recommended to use OmicsBox instead of Blast2GO to benefit from
1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.
