pnpnpn/16speb

16SpeB

By Chun Nin Adam Wong, Patrick Ng, Angela E. Douglas

You can download the archive of this repository at https://github.com/pnpnpn/16SpeB/archive/master.zip

Example

Instructions for a sample run with Mycoplasma hominis

1. Compile palign

    cd 16SpeB_code
    ./compile_palign
   

   Note: This will require g++ on your system. It's pre-installed on Mac OS X and most Linux distribution. For installation of g++ on Debian/Ubuntu:

    sudo apt-get install g++
   

2. Extracting species

   We already added Mycoplasma hominis data within the relevant_species folder.

3. Filtering regions

   Create an output directory called test_Mycoplasma_hominis with mkdir test_Mycoplasma_hominis

    ./isolate_multiregions.pl --midstr='ACTCCTACGGGAGGCAGCA' --rightstr='GTCGTCAGCTCGTGYYG' --rightcoord=1061 --midcoord=338 --right-trimneg=258 --right-trimpos=0 --mid-trimneg=270 --mid-trimpos=0 --longlen-trimneg=270 --longlen-trimpos=1000 --offsetleft=100 --offsetright=100 --fsa=relevant_species/Mycoplasma_hominis.fsa --longlen-fsa=test_Mycoplasma_hominis/Mycoplasma_hominis_raw_16s.fsa --mid-fsa=test_Mycoplasma_hominis/Mycoplasma_hominis_raw_v2.fsa --right-fsa=test_Mycoplasma_hominis/Mycoplasma_hominis_raw_v6.fsa
   

4. Removing exact duplicates within intra-species

    ./filter_duplicates_within_intra_species.pl --fsa=test_Mycoplasma_hominis/Mycoplasma_hominis_raw_16s.fsa --species=Mycoplasma_hominis --nobadwords --auxin=test_Mycoplasma_hominis/Mycoplasma_hominis_raw_v6.fsa --auxout=test_Mycoplasma_hominis/Mycoplasma_hominis_nondup_v6.fsa
   

5. Computing intra-species PID

    ./compute_intra_species_pid_distrib.pl --iters=100 --dir=test_Mycoplasma_hominis --genus=Mycoplasma
   

Manual

A more detailed manual can be found at 16SpeB_manual.doc