fetchSRA.sh | 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
validateSRA.sh | 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 | run filterLen.py with the correct module and input settings | genome of interest | genome filtered at X bp per scaffold |
repeatModeler.sh | Create a de novo repeats library for a genome | filtered genome in fasta format | repeats library entitled conseni.fa.classified |
splitfasta.sh | Reduce the running time for repeatmasker by splitting the genome into pieces | filtered genome in fasta format | multiple pieces of filtered genome |
repeatmasker.sh | Softmask the regions in the genome recognized as repetitive | a piece of the filtered genome | softmasked piece of genome |
concat.sh | Recombine all of the softmasked pieces of the genome | all sm pieces of the genome | One recombined softmasked genome |
