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Quality Assessment of DNA-Seq De Novo Assemblies using QUAST

Genetic Variation studies often involve analyzing samples from a previously studied species. For instance, it is of interest to examine genomes of various cultivars, strains, or populations of the same species. In such cases, it may be necessary to perform de novo DNA-Seq assembly to obtain the genome of the sequenced organisms, even if a reference genome is available. To

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Predict coding regions within transcripts in OmicsBox with TransDecoder

Most transcripts assembled from eukaryotic and prokaryotic RNA-Seq data are expected to code for proteins. The most practical procedure to identify likely coding transcripts is a sequence homology search, such as by BLASTX, against sequences from well-annotated and related species. Predicting coding regions is crucial to determine the molecular role that transcripts play in the cell. Unfortunately, such well-annotated nearby

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Cell-Type Identification via Functional Enrichment Analysis of Single-Cell RNA-Seq Data

  Single-cell RNA sequencing (scRNA-seq) has proven its usefulness in deciphering biological processes. Since it allows the study of samples at the cell level, it provides a more detailed view of the underlying biology.  A nearly mandatory step in any scRNA-seq analysis is to identify the cell types present in the analyzed samples so further biological insights can be obtained.

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metatranscriptomics SortMeRNA OmicsBox rRNA ribosomal removal filtering

rRNA Removal with SortMeRNA in OmicsBox

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

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Contaminant Removal with Bowtie2 in OmicsBox

Metagenomics Contaminant Removal with Bowtie

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

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IsoSeq long-read analysis

IsoSeq De-Novo Isoform Discovery with OmicsBox

Introduction The IsoSeq sequencing method produces full-length transcripts using Single Molecule, Real-Time (SMRT) Sequencing. Long read lengths allow sequencing of full-length transcripts up to 10 kb or longer, removing the need for transcript assembly or inferencing. Therefore, unlike traditional short-read methods, IsoSeq provides a more accurate and complete view of gene expression and alternative splicing events. This comprehensive understanding of

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Gene Prediction Augustus OmicsBox

Eukaryotic Gene Finding with OmicsBox

Introduction Given a new genome, one of the first and most important tasks is determining the structure of its protein-coding genes. Ab initio gene prediction algorithms play a critical role because they produce gene structures quickly, inexpensively, and remarkably reliable. In OmicsBox, the Eukaryotic Gene Finding application is based on AUGUSTUS, which is one of the most accurate programs for

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