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Long read LongQC

Quality Assessment with LongQC

Specific tools for a new generation of sequencing Third Generation Sequencing (TGS) is getting a notable increase in relevance by surpassing some of the limitations of NGS technologies. In that sense, the main feature of TGS is the capacity to produce much longer reads than NGS. These long reads facilitate the assembly of complex genomes and the study of alternative

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Long Read Transcriptome with SQANTI3

Transcriptome Analysis with SQANTI3

Transcriptome analysis is a challenging bioinformatic problem. In eukaryotic transcriptomes, alternative splicing and alternative polyadenylation are the most complex issues. Genome-wide analysis of alternative splicing has been studied with short-read RNA sequencing for a while. Nevertheless, this technology needs a subsequent assembly, which is difficult to be resolved in ambiguities in complex loci.

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Biobam receives a grant from the Valencian Innovation Agency – AVI

  We are proud to announce that we have received a grant from the Valencian Innovation Agency – AVI Our I+D+i project “EVOLUTION OF THE COMPANY’S CLOUD SYSTEM TOWARDS AN ADVANCED ELASTIC PLATFORM FOR HIGH-PERFORMANCE COMPUTING AND MASSIVE SEQUENCING DATA PROCESSING” has received a grant from the Valencian Innovation Agency (AVI) in the line L3 Industrial Doctorate (innodocto) to support

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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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