Atropos statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

Atropos specifications


Unique identifier OMICS_20869
Name Atropos
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.1.19
Stability Stable
Cython; Optional: pytest, progressbar2 or tqdm, pysam (SAM/BAM input), khmer (pip install khmer) (for detecting low-frequency adapter contamination), jinja2 (for user-defined report formats)
Maintained Yes



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  • person_outline John Didion <>

Additional information

Publication for Atropos

Atropos in publication

PMCID: 5827986
PMID: 29482639
DOI: 10.1186/s40168-018-0426-3

[…] were processed using an in-house modular workflow employing snakemake [] (, commit 1c393f4). first, reads were trimmed and quality filtered using atropos v 1.1.5, a fork of cutadapt []. reads aligning to the host genome (grch38.p7) were identified using bowtie 2 v2.3.0 [] with parameters set by the flag—very sensitive local. a total of seven […]

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Atropos institution(s)
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
Atropos funding source(s)
Supported by the NIH intramural program. Additionally, the American Diabetes Association (1-17-PDF-100) and a grant from the Knut and Alice Wallenberg Foundation.

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