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Read realignment software tools | RNA sequencing data analysis

RNA-seq realignment programs have been constructed to address the common causes of systematic artifacts in RNA-seq library preparation, sequencing and alignment.

G T A T C G C T A
MMR
Desktop

MMR MultiMapper Resolution

A post-processor for BAM files, resolving ambiguous alignment locations. MMR…

A post-processor for BAM files, resolving ambiguous alignment locations. MMR infers optimal mapping locations from the coverage density of other mapped reads. Filtering alignments with MMR can…

G T A T C G C T A
RNASequel
Desktop

RNASequel

Runs as a post-processing step in conjunction with an RNA-seq aligner and…

Runs as a post-processing step in conjunction with an RNA-seq aligner and systematically corrects common alignment artifacts. Its key innovations are a two-pass splice junction alignment system that…

G T A T C G C T A
TopHat-Recondit…
Desktop

TopHat-Recondition

Enables easy and fast post-processing for TopHat unmapped reads. The tool can…

Enables easy and fast post-processing for TopHat unmapped reads. The tool can be used to process TopHat-written unmapped reads to make them compatible with downstream tools such as samtools, the…

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