Automated script for virus discovery
Supported inputs: fasta, fastq or fastq.gz. Run on command line as: virus_pipe_accurate.sh your_file.fastq genome_to_map_to
Scripts automates Trimmomatic-0.36, fastqc, Trinity, bwa, samtools, fasta_formatter, cap3, blastn, blastx, pulling out virus reads and adding taxonomic information from ICTV and NCBI. Files are gzipped along the way to save physical memory space.
To run use virus_piple.sh you will need to first use build_dictionary.sh to create a genomic index that can be added to virus_pipe.sh, on line 42 replace "genome_to_map_to" with key you would like to use, and locaiton with the location of the index files
Additional scripts: crawler.sh: provides an example of moving within the output file structure to pull out, delete or change files.