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 |
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 |
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 |
repeatmasker.sh | mask | Use [RepeatMasker] to softmask the regions in the genome recognized as repetitive | a piece of the filtered genome, repeat library generated by [RepeatModeler](http://www.repeatmasker.org/RepeatModeler/) | softmasked piece of genome |
splitfasta.sh | mask | Reduce the running time for repeatmasker by splitting the genome into pieces | filtered genome in fasta format | multiple pieces of filtered genome |
repeatmasker.sh | mask | Softmask the regions in the genome recognized as repetitive | a piece of the filtered genome | softmasked piece of genome |
concat.sh | mask | Recombine all of the softmasked pieces of the genome | all sm pieces of the genome | One recombined softmasked genome |
