title: Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.
abstract: BACKGROUND
  The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI. Alternatively, UMIs can be combined with the sample barcodes into composite barcodes, or with standard Illumina® indexing. Subsequent analysis must take read duplicates and sample identity into account, by identifying UMIs.
  
  
  RESULTS
  Existing tools do not support these complex barcoding configurations and custom code development is frequently required. Here, we present Je, a suite of tools that accommodates complex barcoding strategies, extracts UMIs and filters read duplicates taking UMIs into account. Using Je on publicly available scRNA-seq and iCLIP data containing UMIs, the number of unique reads increased by up to 36 %, compared to when UMIs are ignored.
  
  
  CONCLUSIONS
  Je is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je . Je can also be easily installed in Galaxy through the Galaxy toolshed.
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany. charles.girardot@embl.de.
authors.forename: Charles
authors.identifier: http://orcid.org/0000-0003-4301-3920
authors.initials: C
authors.lastname: Girardot
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany.
authors.forename: Jelle
authors.initials: J
authors.lastname: Scholtalbers
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany.
authors.forename: Sajoscha
authors.initials: S
authors.lastname: Sauer
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany.
authors.forename: Shu-Yi
authors.initials: SY
authors.lastname: Su
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany.
authors.forename: Eileen E M
authors.initials: EE
authors.lastname: Furlong
mesh_terms: D001330:Electronic Data Processing / Q000379:methods*; D015723:Gene Library; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Duplicates; Genomics; Multiplexing; NGS; Software; UMI