Tips, Tricks and Video Tutorial

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

In analyzing long-read RNA-sequencing data, defining a custom transcriptome by identifying novel isoforms is a complex yet essential task that can have far-reaching consequences for any downstream analyses. As long reads allow researchers to examine isoform diversity in significantly greater detail than short reads, long-read sequencing often reveals a large variety of isoforms not yet present in reference annotations, even

The Burrows-Wheeler Alignment algorithm (BWA) is a tool designed to align short DNA and RNA reads. BWA is based on the Burrows-Wheeler Transform (BWT), an algorithm designed to rearrange sequences into runs of similar characters to improve data compression and efficient sequence alignment in Bioinformatics. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads

In the field of bioinformatics and genomic research, data representation is a critical aspect that influences the ease and accuracy of analysis. Two common file formats used in genomic data representation are Gene Transfer Format (GTF) and General Feature Format (GFF). While they may seem similar at a glance, there are distinct differences between these two formats that are crucial