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Docker Pipelines for RNA-Seq Alignment and Analyses

Docker Pipelines for RNA-Seq Alignment and Analyses

Background: Docker (https://www.docker.com) is an application that packages binary executables and scripts into modules (containers) with their software dependencies. Containers can be freely mixed and matched to form workflows that give identical results on any platform which supports Docker. The ...

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VirusDetect – a new pipeline for virus identification

VirusDetect – a new pipeline for virus identification

Researchers studying the viruses that affect agricultural production or human health now have a new tool for investigating where viruses have spread, on a local, national, or even global scale. VirusDetect is a free, open-source bioinformatics pipeline that can efficiently ...

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The PARA-suite – PAR-CLIP specific sequence read simulation and processing

The PARA-suite – PAR-CLIP specific sequence read simulation and processing

Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein-RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into ...

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SPIRE – a modular pipeline for eQTL analysis of RNA-Seq data

SPIRE – a modular pipeline for eQTL analysis of RNA-Seq data

The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it ...

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SAMSA – a comprehensive metatranscriptome analysis pipeline

SAMSA – a comprehensive metatranscriptome analysis pipeline

Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated ...

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ChloroSeq – an organelle RNA-Seq bioinformatics pipeline

ChloroSeq – an organelle RNA-Seq bioinformatics pipeline

Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. ...

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