SISRS2.0 Tutorial¶

SISRS v2.0 can be run in two different ways:

Continuous Run
- This option may take a longer amount of time to run
Split Run
- This option allows the user to go through and check the output at each step

Note: All examples are working on the SISRS_Small.zip that was provided in the github. We are assuming that you have already done a git pull from SISRS and unzipped the small data set.

Continuous Run Example¶

This section will give you an example on how to run SISRS using the continues run option that is implemented. As you move down in the list of commands more arguments get added to show more complex examples:

#Run SISRS with a genome size estimate of 100 MB
> python sisrs.py -d ./SISRS_Small/ -gs 100000000
> python sisrs.py --data ./SISRS_Small/ --genomeSize 100000000


#Run SISRS with a genome size estimate of 2GB, 20 processors, and pre-trimmed reads
> python sisrs.py -d ./SISRS_Small/ -gs 2000000000 -p 20 -trm
> python sisrs.py --data ./SISRS_Small/ --genomeSize 2000000000 --processors 20 -trm


#Run SISRS with a genome size estimate of 100bp, 10 processors, allowing 2/3 homozygosity,
# a minimum read coverage of two reads, and allowing one taxon to be missing for any given
# site in the final alignment
> python sisrs.py -d ./SISRS_Small/ -gs 100 -p 10 -thresh .66 -mr 2 -ms 1
> python sisrs.py --data ./SISRS_Small/ --genomeSize 100 --processors 10 --threshold .66 --minread 2 --missing 1

#Run SISRS with a genome size estimate of 100bp, 10 processors, allowing 2/3 homozygosity,
# a minimum read coverage of two reads, and allowing 1-6 taxon to be missing for any given
# site in the final alignment
> python sisrs.py -d ./SISRS_Small/ -gs 100 -p 10 -thresh .66 -mr 2 -ms 1-6
> python sisrs.py --data ./SISRS_Small/ --genomeSize 100 --processors 10 --threshold .66 --minread 2 --missing 1-6

Split Run Example¶

The section is split up into subsections based on each of the seven scripts that defines the most important parts of the SISRS software. Each subsection will give you an example on how to run that individual script based on the some general command line options and some more complex options.

sisrs_01_folder_setup¶

> python scripts/sisrs_01_folder_setup.py -d /SISRS_Small/
> python scripts/sisrs_01_folder_setup.py -data /SISRS_Small/

#If data in already trimmed...
> python scripts/sisrs_01_folder_setup.py -d /SISRS_Small/ -trm
> python scripts/sisrs_01_folder_setup.py -data /SISRS_Small/ --trimmed
You also have the option of using the -id flag which will require you yo manually move your data to the correct location after the script has completed running.
> python scripts/sisrs_01_folder_setup.py -id TaxonIDs

sisrs_02_read_trimmer¶

> python scripts/sisrs_02_read_trimmer.py -p <# processors>
> python scripts/sisrs_02_read_trimmer.py --processors <# processors>

sisrs_03_read_subsetter¶

#For a SISRS run on ape species (with ~3.5Gb genome)
> python scripts/sisrs_03_read_subsetter.py -gs 3500000000
> python scripts/sisrs_03_read_subsetter.py --genomeSize 3500000000

sisrs_04_ray_composite¶

#1 node, 20 processors per node
> python scripts/sisrs_04_ray_composite.py -p 20
> python scripts/sisrs_04_ray_composite.py --processors 20

#3 nodes, 50 processors per node
> python scripts/sisrs_04_ray_composite.py -p 150
> python scripts/sisrs_04_ray_composite.py --processors 150

sisrs_05_setup_sisrs¶

# 20 processors, 3 reads required to call a site, 100% homozygosity per species
> python scripts/sisrs_05_setup_sisrs.py -p 20 -mr 3 -thrs 1

# 10 processors, 5 reads required to call a site, 99% homozygosity per species
> python scripts/sisrs_05_setup_sisrs.py --processors 10 --minread 5 --threshold .99

sisrs_06_run_sisrs¶

> python scripts/sisrs_06_run_sisrs.py

sisrs_07_output_sisrs¶

#0 missing taxa allowed
> python scripts/sisrs_07_output_sisrs.py

#3 missing taxa allowed
> python scripts/sisrs_07_output_sisrs.py -ms 3

# 3, 4, 5, and 6 missing taxa allowed
> python scripts/sisrs_07_output_sisrs.py --missing 3-6