StrainSeeker - Download and install
Downloadable version of StrainSeeker is for detecting bacterial strains on your own UNIX server. If you are interested in analyzing large amounts of data or want to create your own database, this is the version for you. For a simple preview you can use the online version of StrainSeeker.
For your reference, we also provide a manual and in case of problems or suggestions, please contact us.
Installing instructions
- StrainSeeker requires both PERL and R - please install those first
- To run StrainSeeker, please first download one of the database and programs (listed below - 1. and 2.).
- Extract all the files into a separate directory for StrainSeeker. Database resides in its own subdirectory (directory is already created, just use tar -xzvf to unpack)
- All the programs and scripts should be under the main directory, but not IN the database directory
- Finally, just run either "perl seeker.pl" for detecting strains or "perl builder.pl" if you wish to build your own database.
Downloads
All downloads shown here are for UNIX only (GenomeTester4 programs are compiled for UNIX).
OSX versions will soon be available.
StrainSeeker for Windows will not be available.
- Database - pre-built from 4,324 NCBI RefSeq strains (w32) | (18.5 GB) Last update 10-feb-2016, recommended
- Database - pre-built from 4,324 NCBI RefSeq strains (w16) | (4.5 GB) Last update 21-feb-2017
- StrainSeeker programs and scripts Last update 10-feb-2016
- Optional data files and scripts Last update 10-feb-2016
- Blacklist - list file containing human and plasmid k-mers | (w = 32). Optional while building a custom database (13 GB)
- Newick-format tree (4,324 strains) | For your reference only, NOT NEEDED for StrainSeeker
- Info file - database info file in case yours is missing/corrupted