FASTASTIC V1.0.0 README

FASTASTIC is a program that takes a .fastq prokaryotic genome read file and automatically runs it through FastQC for quality check of reads and SPAdes to be assembled. The resulting FASTA file from SPAdes is then run through QUAST to check assembly quality and Prokka to annotate the assembly.

Dependencies

FASTASTIC requires the following dependencies:

1. SPAdes
2. FastQC
3. QUAST
4. Prokka

By default, FASTASTIC will assume the executable (driver) files are located in the root project directory. If you have the dependencies downloaded elsewhere, pass the locations of the executables using arguments -s, -p and -q.

Usage

1. Ensure that you have Python v3.5
2. Ensure that your input file is .fastq format
3. Run using python3 fastastic.py with the appropriate arguments

Check the appropriate parameters using python3 fastastic.py --help.

Example

Below is an example use case, utilizing the example test.fastq file provided in the repository:

python3 fastastic.py -s SPAdes-3.8.1-Darwin/bin/spades.py -q quast-4.3/quast.py -p prokka-1.11/bin/prokka test.fastq

Contact

For questions regarding the code, please contact the repository owner