Mandalorion specifications


Unique identifier OMICS_30059
Name Mandalorion
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Some read alignments.
Input format FASTA
Output data A file containing consensus reads and a second containing subreads.
Output format FASTA
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 2.0
Stability Stable
minimap2, racon
Maintained Yes




No version available


  • person_outline Christopher Vollmers

Mandalorion citation


Nanopore long read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Nat Commun
PMCID: 5524981
PMID: 28722025
DOI: 10.1038/ncomms16027

[…] . Because standard gene quantification tools (for example, STAR, Cufflinks) are not compatible with nanopore reads, we aligned the ONT 2D reads using BLAT and quantified gene expression using our own Mandalorion pipeline. Mandalorion determines how many reads overlap with the exons of a gene to produce a Reads Per Gene per 10 K reads (RPG10K) value. As ONT 2D reads are long enough to span the full […]

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