These scripts are still under developement, but are available for use.
Copyright 2019 by Shawn Rupp
Download NCBI Blast+ here
pip install -y openpyxl pandas
git clone https://github.com/icwells/blastnWrapper.git
Make a copy of example_config.txt and fill in the fields with the path to appropriate file or directory.
blast bin directory Directory containing Blast binaries.
reference genome Path to Reference genome used for construcitng database.
blast database Path and name of blast database (do not include a file extension).
input fastq files Directory containing query of fastq files. They may or may not be gzipped.
output directory Path to directory where output will be written.
python blastnWrapper.py --{makedb/blastn/summary} -c path_to_config
-h, --help show this help message and exit.
--makedb Makes database for blasting with provided fasta file. Output is written to the blast database given in the config file.
--blastn Calls blastn on provided input files. Runs summary by default.
--summary Produces summary of directory of ublast results.
-c C Path to configuration file.
-t 1 Number of threads to run blast.
-i I Path to input variants file.
-p 0.95 Minimum percent identity.
-e 0.00001 Maximum expected value.
-v Print version info.