fetchSRA.sh | gather | Gather data from multiple SRR runs from ncbi | 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
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 | The same input file you ran for fetchSRA | an output and error file assuring that all runs were downloaded correctly |
filtersubmit.sh | filter | run filterLen.py with the correct module and input settings | genome of interest | genome filtered at X bp per scaffold |
repeatModeler.sh | mask | Create a de novo repeats library for a genome | filtered genome in fasta format | repeats library entitled conseni.fa.classified |
