UMI-tools pipeline

UMI-tools specifications


Unique identifier OMICS_15010
Name UMI-tools
Alternative name Unique Molecular Identifiers-tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM, FASTQ
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements Numpy, Pandas, cython, pysam, future, setuptools
Maintained Yes



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  • person_outline Ian Sudbery <>

Publication for Unique Molecular Identifiers-tools

UMI-tools IN pipeline

PMCID: 5789978
PMID: 29382943
DOI: 10.1038/s41598-018-20282-8

[…] as an additional read. the uid sequence was added to the read name for each sequence in the fastq file. individual reads were mapped to hg19 using bwa mem (v0.7.5a) keeping only primary mappings. umi-tools (v0.3.6) in group mode and directional method were used to cluster the identical uid-genomic-position tags including those with minor sequence variations attributable to pcr errors (thereby […]

UMI-tools institution(s)
Computational Genomics Analysis and Training Programme, MRC WIMM Centre for Computational Biology, University of Oxford, John Radcliffe Hospital/Headley Way, Oxford, UK; Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, UK
UMI-tools funding source(s)
Supported by an MRC programme grant [G1000902].

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