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IMSA specifications


Unique identifier OMICS_15201
Alternative name Integrated Metagenomic Sequence Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Takes input sequence from high throughput datasets and utilizes a user-defined host database to filter out host sequence.
Output data Assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA can also output the specific sequence reads assigned to a taxon of interest for downstream analysis.
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Aleksey Porollo

Publications for Integrated Metagenomic Sequence Analysis

IMSA citations


Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] f minutes (12 workflows: CaPSID, Clinical PathoScope, DUDes, EnsembleAssembler, FACS, Kraken, LMAT, Metavir, MetLab, SMART, Taxonomer and Virana), or hours (19 workflows: Giant Virus Finder, GOTTCHA, IMSA, MEGAN, MePIC, MetaShot, Metavir 2, NBC, ProViDE, Readscan, Rega Typing Tool, RIEMS, RINS, SLIM, SURPI, Taxy-Pro, “Unknown pathogens from mixed clinical samples,” VIP and ViromeScan), or even day […]


Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

BMC Bioinformatics
PMCID: 4131054
PMID: 25091138
DOI: 10.1186/1471-2105-15-262

[…] sed on their ability to rapidly identify the pathogens present in the clinical datasets described above. We also considered several published metagenomic-like pipelines such as CloVR-Metagenomics [], IMSA [], LMAT [], and metAMOS [] in the context of pathogen identification. These methods were of limited use in this context because of their significantly longer run times (see Results). Additionall […]


High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis

PMCID: 4102619
PMID: 24608988
DOI: 10.1038/jid.2014.127

[…] the human genome (hg19). Over 99% of the total readset was derived from human or nonhuman primate in both SSc and control samples. On average, 4×105 reads remained per sample after host filtering (). IMSA mapped reads to the NCBI non-redundant nucleotide (nt) database and generated taxonomy reports. In this analysis, each taxonomic level is given a score based on the number of reads aligning to se […]


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IMSA institution(s)
Department of Dermatology, University of California San Francisco, San Francisco, CA, USA; Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds, UK; Department of Electrical Engineering and Computing Systems, University of Cincinnati, Cincinnati, OH, USA; The Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
IMSA funding source(s)
This work was supported by the National Institutes of Health [5R01HL119190].

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