umitools statistics

info info

Citations per year

info

Popular tool citations

chevron_left Error correction Duplicate read removal UMI processing chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

umitools specifications

Information


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

Download


download.png

Versioning


No version available

Maintainers


  • 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

 (2)
library_books

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

2017
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 […]

library_books

Global analysis of RNA cleavage by 5′ hydroxyl RNA sequencing

2015
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 (https://github.com/brwnj/umitools). processed reads were aligned to the s. cerevisiae genome (saccer1) with bowtie () and visualized in the ucsc genome browser (). coverage signals […]


Want to access the full list of citations?
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

umitools reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review umitools