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JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of ...

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FANSe2: A Robust Tool for Quantitative NGS Applications

FANSe2: A Robust Tool for Quantitative NGS Applications

Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) ...

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Hobbes2 – for fast and accurate alignment of NGS reads

Hobbes2 – for fast and accurate alignment of NGS reads

Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in many sequencing applications. Popular read mappers, such as Bowtie ...

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