Microbial Profile Generation

foward reads: https://d28rh4a8wq0iu5.cloudfront.net/bioinfo/SRR292678sub_S1_L001_R1_001.fastq.gz
reverse reads: https://d28rh4a8wq0iu5.cloudfront.net/bioinfo/SRR292678sub_S1_L001_R2_001.fastq.gz

SeqPro requires:
-Velvet
-BWA-mem
-BLAST
-MySQL loaded with MediaDB (Note: User must change the MySQL db user, password, and database to match their local machine's in mediaQuery.py)
-CGE's ResFinder, VirulenceFinder, PlasmidFinder, SerotypeFinder Databases
-CBA's 16S rRNA Database
-samtools

python configure.py

usage: SeqPro.py [-h] -f1 FASTQ1 [-f2 FASTQ2] -rt READ_TYPE [-r REFERENCE] [-v]

optional arguments:
-h, --help show this help message and exit
-f1 FASTQ1, --fastq1 FASTQ1
forward fastq reads from bacterial sample
-f2 FASTQ2, --fastq2 FASTQ2
reverse fastq reads from bacterial sample
-rt READ_TYPE, --read_type READ_TYPE
type of read library input, s=single end, p=paired
end, m=mate pair
-r REFERENCE, --reference REFERENCE
optional reference fasta to perform assembly against
-v, --verbosity increase output verbosity