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CATCh – an ensemble classifier for chimera detection in 16S rRNA sequencing studies

CATCh – an ensemble classifier for chimera detection in 16S rRNA sequencing studies

In this study, researchers from the University of Michigan present a method to utilize GPMDB identification frequencies and RNA-Seq transcri...

In this study, researchers from the University of Michigan present a method to utilize GPMDB identification frequencies and RNA-Seq transcri...

Here researchers from the University of Freiburg introduce BlockClust, an efficient approach to detect transcripts with similar processing p...

Here researchers from the University of Freiburg introduce BlockClust, an efficient approach to detect transcripts with similar processing p...

IRcall and IRclassifier – two methods for flexible detection of intron retention events from RNA-Seq data - The emergence of next-generation RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate detection of intron retention (IR) events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS) studies....

IRcall and IRclassifier – two methods for flexible detection of intron retention events from RNA-Seq data - The emergence of next-generation RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate detection of intron retention (IR) events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS) studies....

SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)...

SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)...

Researchers at the University of North Carolina, Chapel Hill found that chimeric RNA-cDNA fragments can also be detected at 5′ end stem-loop...

Researchers at the University of North Carolina, Chapel Hill found that chimeric RNA-cDNA fragments can also be detected at 5′ end stem-loop...

PrimerView – forward and reverse primer design from multi-sequence datasets - High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer walking experiments. Batch primer design is also required in validation experiments from RNA-seq transcriptome sequencing projects, as well as in generating probes for microarray experiments.  The growing…

PrimerView – forward and reverse primer design from multi-sequence datasets - High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer walking experiments. Batch primer design is also required in validation experiments from RNA-seq transcriptome sequencing projects, as well as in generating probes for microarray experiments. The growing…

To improve the efficiency of adapter trimming, researchers at the Institute of Plant Quarantine Research, Beijing devised a novel algorithm,...

To improve the efficiency of adapter trimming, researchers at the Institute of Plant Quarantine Research, Beijing devised a novel algorithm,...

SimSeq – A Nonparametric Approach to Simulation of RNA-Sequence Datasets - RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method...

SimSeq – A Nonparametric Approach to Simulation of RNA-Sequence Datasets - RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method...

Kpath ‐ statistical reference-based compression for short reads - Storing, transmitting, and archiving data produced by next generation sequencing is a significant computational burden. New compression techniques tailored to short-read sequence data are needed.  Researchers from Carnegie Mellon University and Stony Brook University have devloped an approach to compression that reduces the difficulty of managing large-scale sequencing data. This novel approach sits ...

Kpath ‐ statistical reference-based compression for short reads - Storing, transmitting, and archiving data produced by next generation sequencing is a significant computational burden. New compression techniques tailored to short-read sequence data are needed. Researchers from Carnegie Mellon University and Stony Brook University have devloped an approach to compression that reduces the difficulty of managing large-scale sequencing data. This novel approach sits ...

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