fetchSRA.sh | gather | Gather data from multiple NCBI SRRs (**S**equence **R**ead archive **R**un accessions) | Text file containing the specific SRR runs that you want to download | raw reads in .fastq format | the option `--split-files` in line 22 must be removed if gathered data is not paired
validateSRA.sh | gather | To validate that the correct files have been downloaded from NCBI | Text file containing the specific SRR runs that you want to download | an output and error file confirming that all runs were downloaded correctly |
validateSRA.sh | gather | Validates that the correct files have been downloaded from NCBI | Text file containing the specific SRR runs that you want to download | an output and error file confirming that all runs were downloaded correctly |
filtersubmit.sh | filter | run filterLen.py with the correct module and input settings to remove small scaffolds from genome assembly | genome assembly of interest | genome assembly excluding scaffolds < 500 bp |
repeatModeler.sh | mask | Use [RepeatModeler](http://www.repeatmasker.org/RepeatModeler/) to generate a de novo repeats library for a genome | filtered genome assembly in fasta format | repeats library suffixed conseni.fa.classified |
concat.sh | mask | Concatenate all of the pieces of the split and softmasked genome | all sm pieces of the genome | Softmasked genome assembly |
