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Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Enrique Presa May 22, 2023

Transcriptome reconstruction is a challenging bioinformatic problem. The development of long-read sequencing technologies has made it easier to solve this issue thanks to the possibility of having transcripts entirely contained in a read. In addition, different algorithms have emerged to generate transcriptomes from long-read datasets, such as FLAIR and StringTie2. Both tools can be used for transcriptome reconstruction with long-read data.

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

Enrique Presa May 1, 2023

The study of genetic variation is fundamental in genomics research as it enables the comprehension of mutation causes and effects in the diversity of life. However, research in this field is well-developed in model organisms, while non-model organisms lack sufficient guidance for a consistent variant analysis pipeline. OmicsBox is a robust tool for investigating genetic variation in non-model organisms, facilitating

GWAS with OmicsBox

Enrique Presa April 24, 2023

Genome-Wide Association Studies (GWAS) are a valuable approach to investigating the relationship between genetic variations and phenotypic traits. However, due to many different analysis options, performing GWAS can be challenging, especially for researchers without a strong background in statistics or bioinformatics. OmicsBox’s Genetic Variation Module provides a solution by offering a user-friendly interface to powerful analysis tools. It includes a

KEGG Pathways in OmicsBox

Paula Cubilles March 22, 2023

This article explains how to analyse your data with the help of KEGG Pathways with OmicsBox. The free KEGG pathway app can be installed via the App Manager.

Quality Assessment of DNA-Seq De Novo Assemblies using QUAST

Marta Benegas Coll March 7, 2023

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

LongTREC – BioBam member of a new ITN initiative

Paula Cubilles March 6, 2023

The European Union’s ITN initiative provides funding and hosting opportunities for Ph.D. students from around the world. As previously noted in one of our earlier posts, the ITN brings together some of the most prestigious institutions in the European Union to work on innovative research projects. Today we are pleased to present you the LongTREC project. Its primary objective is

OmicsBox 3.0 Release: New Module and Features

Paula Cubilles February 15, 2023

Once again we are pleased to announce the latest update of OmicsBox 3.0. The whole BioBam team has worked to bring the new version of the BioBam bioinformatics solution to life. We proudly present the Genetic Variation Module as the highlight of OmicsBox 3.0. This module enables variant calling, filtering, and annotation, as well as the association of genetic variations

BioBam Team at PAG30 in San Diego

Paula Cubilles February 9, 2023

This January, the BioBam team had the pleasure of attending the Plant and Animal Genome Conference in San Diego, California. This international event is a MUST for everyone working in the Plant and Animal Genomics space. For us, coming back to PAG after the Covid break was a great opportunity to get re-connected to the community and catch up with

Predict coding regions within transcripts in OmicsBox with TransDecoder

Enrique Presa February 4, 2023

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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Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

GWAS with OmicsBox

KEGG Pathways in OmicsBox

Quality Assessment of DNA-Seq De Novo Assemblies using QUAST

LongTREC – BioBam member of a new ITN initiative

OmicsBox 3.0 Release: New Module and Features

BioBam Team at PAG30 in San Diego

Predict coding regions within transcripts in OmicsBox with TransDecoder

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