Phineus as a generic tool for repetitive sequencing projects

Phineus can be used for any projects where there is repetitive sequencing of the same DNA fragments (or a single DNA fragment) from many isolates/individuals and for managing these projects by organisng all of the strain information, sequence trace files, edited sequences etc in a database. Pre-optimised schema are provided for some uses, but schema for other purposes can easily be set up by the user and stored within Phineus. Although mainly designed for projects where a single pair of sequences are obtained for each DNA fragment, Phineus currently has the ability to provide edited and trimmed sequences by assembling multiple reads. It can also be used where single reads are considered acceptable, providing there are no ambiguous bases.

Specific uses of Phineus

MLST projects - http://www.mlst.net

• Ability to select schema pre-optimised for the processing and analysis of MLST data from isolates of Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Enterococcus species, Burkholderia pseudomallei etc.
• Ability within Phineus to interrogate the above MLST databases to obtain allele and ST numbers, to identify identical or similar strains in the MLST database, and to compare the new isolates with those in your own database or the entire MLST database using eBURST.

NG-MAST - http://www.ng-mast.net

• Optimised schema for processing and trimming sequence traces for Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) and for comparing the edited sequences with those in the NG-MAST database .

Generic uses of Phineus for repetitive sequencing projects

User-defined settings for processing gene fragments
In the above applications single forward and reverse reads of a gene fragment are used to obtain the edited and correctly trimmed fragments using pre-stored schema, which contain the information needed to process and trim the gene fragments used in the above MLST schemes or in NG-MAST. Phineus can also be used to process and trim other gene fragments by simply providing the information needed to process and trim the gene fragments (sequences, location of trim points etc). These are stored within Phineus allowing the user to use these settings as their default schema.

Ability to assemble larger DNA fragments from multiple sequences
The ability to process and trim a pair of sequences can be extended to situations where several sequence reads are needed to assemble a larger DNA fragment. At present Phineus can process, assemble and trim up to eight sequences (four forward and four reverse trace files) to allow its use in repetitive sequencing projects involving larger gene fragments (up to about 2-kb). If there is demand, the ability to assemble more than eight sequences could be added.

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