Despite the rapid advance in single-cell RNA sequencing (scRNA-seq) technologies within the last decade, single-cell transcriptome analysis workflows have primarily used gene expression data while...
Read More »CircAST – full-length assembly and quantification of alternatively spliced isoforms in circular RNAs
Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms at the same locus. However...
Read More »Ryūtō – network-flow based transcriptome reconstruction
The rapid increase in High-throughput sequencing of RNA (RNA-seq) has led to tremendous improvements in the detection and reconstruction of both expressed coding and non-coding RNA...
Read More »CoCo – RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads
Next generation sequencing techiques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Here ...
Read More »Best RNA-Seq aligner: A comparison of mapping tools
RNA-Seq has replaced microarrays for many applications in the area of biomarker discovery. The prices have been fallen substantially in recent years. The sequence data allows to extract more information than gene expression only. And there is no requirement that ...
Read More »TransFlow – a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is...
Read More »Machine learning meets genome assembly
With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which ...
Read More »STAble – a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow
De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism...
Read More »Necklace – combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis
RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating...
Read More »RNA-seq alignment – where methodological progress can still occur
Many tools are available for RNA-seq alignment and expression quantification, with comparative value being hard to establish. Benchmarking assessments often highlight methods' good performance, but are focused on either model data or fail to explain...
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