Items referring to sequence-level data, including genomics, microbiomics, proteomics, etc.

molecular

fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This tool supports both short reads (Illumina, BGI, etc.) and long reads (ONT, PacBio, etc.).

non-collection specific

(Simple) Released

English

MIT License

Zhicheng Li

Changshou He

Shifu Chen

Charles E Melancon III

Yingqiang Li

C++ is a general-purpose programming language created as an extension of the C programming language, supporting object-oriented and generic programming.

fastv: A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data

A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis.

Severe acute respiratory syndrome coronavirus 2

SARS-CoV2

An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.

host organism

Host

Homo sapiens

Infection by an etiologic agent that can be passed between animals and humans.

Zoonotic Infection

Zoonotic infection

A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

disease

Disease

A disease whose physical basis is an infectious disorder

infectious disease

Infectious Disease

A Coronavirus infection that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.

COVID-19

An acute viral infection of the respiratory tract, occurring in isolated cases, in epidemics, or in pandemics; it is caused by serologically different strains of viruses (influenzaviruses) designated A, B, and C, has a 3-day incubation period, and usually lasts for 3 to 10 days. It is marked by inflammation of the nasal mucosa, pharynx, and conjunctiva; headache; myalgia; often fever, chills, and prostration; and occasionally involvement of the myocardium or central nervous system.

influenza

Influenza

The type species of the genus ALPHAINFLUENZAVIRUS that causes influenza and other diseases in humans and animals. Antigenic variation occurs frequently between strains, allowing classification into subtypes and variants. Transmission is usually by aerosol (human and most non-aquatic hosts) or waterborne (ducks). Infected birds shed the virus in their saliva, nasal secretions, and feces.

Influenza A virus

viral Infectious disease

Viruses Infection

sequence collection

Sequence Collection

Tools for initial stages of data processing, usually prior to modeling. Includes pre-processing, cleaning, exploratory analysis.

data preparation

Data Preparation

Vaccine preventable diseases are those infectious diseases that can be prevented by vaccination

vaccine-preventable Disease

Vaccine-Preventable Disease

A respiratory tract infection caused by a virus. Viruses represent the most common causes of upper and lower respiratory tract infections and include rhinoviruses, influenza viruses, parainfluenza viruses, and respiratory syncytial virus.

viral respiratory tract infection

Viral Respiratory Tract Infection

Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.

Viruses

An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.

pathogen

Pathogen

Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.

software

Written programs or procedures or rules and associated documentation pertaining to the operation of a computer system and that are stored in read/write memory.

Package

Topic

Digital Object Type

Apache 2.0

Schema.org vocabulary for structured data on the web

Schema.org

Dublin Core Metadata Initiative Terms - refined elements for precise resource description

DCMI Metadata Terms

Provenance, Authoring and Versioning ontology for metadata about web resources

PAV Ontology

W3C Provenance Ontology for describing provenance information

PROV Ontology

Custom MIDAS vocabulary for epidemiological data and modeling

MIDAS Metadata Vocabulary

Health Level 7 Fast Healthcare Interoperability Resources

HL7 FHIR

Systematized Nomenclature of Medicine Clinical Terms

SNOMED Clinical Terms

LOINC database for laboratory and clinical observations

Logical Observation Identifiers Names and Codes

OBO Foundry ontologies for life sciences and biomedical research

Open Biological and Biomedical Ontology

JSON Schema (Draft 2020-12) defining the structure of MIDAS Catalog JSON-LD metadata records

MIDAS Catalog JSON-LD Schema

Searchable collection of curated datasets and software resources for infectious disease modeling, filterable by disease, topic, location, and time period.

Identifier	URL: https://github.com/OpenGene/fastv
Type	Software Package
Topics/About	Data Preparation Disease Infectious Disease Vaccine-Preventable Disease COVID-19 Influenza Viruses Infection Viral Respiratory Tract Infection COVID-19 Influenza Zoonotic infection Influenza Host Homo sapiens Pathogen Viruses Influenza A virus SARS-CoV2 Sequence Collection
Language	English
License	MIT License
Accessible For Free	TRUE
Biological Scale	molecular
Software Language	C++
Version	0.10.0
HTTP Status Code	200
HTTP Checked On	2026/09/27