Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

BMC Bioinformatics

Software

Jelle Scholtalbers¹  Charles Girardot¹  Sajoscha Sauer¹  Eileen E.M. Furlong¹  Shu-Yi Su¹ 

[1] European Molecular Biology Laboratory, Genome Biology Unit, D-69117, Heidelberg, Germany;

关键词: Software;    Genomics;    NGS;    UMI;    Multiplexing;    Duplicates;   

DOI  :  10.1186/s12859-016-1284-2

 received in 2015-12-01, accepted in 2016-09-28,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsExisting 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.ConclusionsJe 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.

【 授权许可】

CC BY   
© The Author(s). 2016