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README.md

tiptoft container

Main tool: tiptoft

Code repository: https://github.com/andrewjpage/tiptoft

Additional tools as listed by pip freeze:

  • biopython: 1.79
  • pyfastaq: 3.17.0
  • cython: 3.0.12
  • numpy: 1.19.5

Basic information on how to use this tool:

  • executable: tiptoft
  • help: --help
  • version: --version
  • description: Predict plasmids from uncorrected long read data

Additional information: This container includes a pre-downloaded plasmid database. Use tiptoft_database_downloader to download the latest PlasmidFinder database. The database downloader uses the PlasmidFinder Bitbucket repository.

  • AJ Page, T Seemann (2019). TipToft: detecting plasmids contained in uncorrected long read sequencing data. Journal of Open Source Software, 4(35), 1021, https://doi.org/10.21105/joss.01021
  • Carattoli et al, In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing, Antimicrob Agents Chemother. 2014;58(7):3895–3903.
  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421.
  • Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307.

Full documentation: https://github.com/andrewjpage/tiptoft/blob/master/docs/USER_GUIDE.md

Example Usage

Download the plasmid database

tiptoft_database_downloader tiptoftDB_name

Run tiptoft with the downloaded database

tiptoft -d tiptoftDB_name.fa ERS654932_plasmids.fastq.gz

Run tiptoft with the built-in database

tiptoft ERS654932_plasmids.fastq.gz