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umitools specifications


Unique identifier OMICS_26836
Name umitools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
Computer skills Advanced
Version 0.2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Zhiping Weng <>
  • person_outline Phillip Zamore <>
  • person_outline Yu Fu <>

Additional information

Supported in part by National Institutes of Health grants P01HD078253 and R37GM062862 and HD078253.

Publication for umitools

umitools citations


Batch effects and the effective design of single cell gene expression studies

PMCID: 5206706
PMID: 28045081
DOI: 10.1038/srep39921

[…] in base quality at the 3′ end of the reads. thus we removed low quality bases from the 3′ end using sickle with default settings. to handle the umi sequences at the 5′ end of each read, we used umitools to find all reads with a umi of the pattern nnnnnggg (reads without umis were discarded). we then mapped reads to human genome hg19 (only including chromosomes 1–22, x, and y, plus the ercc […]


Global analysis of RNA cleavage by 5′ hydroxyl RNA sequencing

PMCID: 4787814
PMID: 26001965
DOI: 10.1093/nar/gkv536

[…] miseq in a 50 cycle run. raw and processed sequencing data are available at ncbi geo under accession number gse61527., sequences in fastq format were preprocessed to remove molecular indexes using umitools ( processed reads were aligned to the s. cerevisiae genome (saccer1) with bowtie () and visualized in the ucsc genome browser (). coverage signals […]

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umitools institution(s)
Bioinformatics Program, Boston University, Boston, MA, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA; RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA

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