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Kingfisher

bio.tools Bridge

Welcome.

Kingfisher is a fast and flexible program for procurement of sequence files (and their annotations) from public data sources, including the European Nucleotide Archive (ENA), NCBI SRA, Amazon AWS and Google Cloud. It's input is one or more "Run" accessions e.g. DRR001970, or a BioProject accessions e.g. PRJNA621514 or SRP260223.

For more documentation, see https://wwood.github.io/kingfisher-download/

Kingfisher logo

Functions

Data retrieval, Sequence database search (by property) 
# biotools-function
operation:
- term: Data retrieval
  uri: http://edamontology.org/operation_2422
- term: Sequence database search (by property)
  uri: http://edamontology.org/operation_0349
input:
- data:
    term: Accession
    uri: http://edamontology.org/data_2091
  format: []
output:
- data:
    term: Nucleic acid sequence
    uri: http://edamontology.org/data_2977
  format:
  - term: SRA format
    uri: http://edamontology.org/format_3698
  - term: FASTQ
    uri: http://edamontology.org/format_1930
  - term: FASTA
    uri: http://edamontology.org/format_1929
cmd: kingfisher get -r ERR1739691 -m ena-ascp aws-http prefetch