qiime_tools

This repository have collection of tools to process amplicon data.

Demultiplex sequences

You need to demultiplex sequences if you get your sequence like this:

Undetermined_S0_L001_I1_001.fastq.gz
Undetermined_S0_L001_R1_001.fastq.gz
Undetermined_S0_L001_R2_001.fastq.gz

Here, you can use demultiplex_sequences.py to demeltiplex. You will need mapping file (Same file that Qiime reqires)

clean mapping file

python /mnt/research/germs/softwares/qiime_tools/clean_mapping_file.py 190103_Mapping_File_GermWater_Tott_16SF_20181219.txt > clean.mappingfile.txt

Usage

Note: if your barcode matches in reverse complementary, then use option --reverse_complement

python2 /mnt/research/germs/softwares/qiime_tools/demultiplex_sequences.py -m clean.mappingfile.txt -b Undetermined_S0_L001_I1_001.fastq.gz -f Undetermined_S0_L001_R1_001.fastq.gz -r Undetermined_S0_L001_R2_001.fastq.gz -o demeltiplex

Example

python demultiplex_sequences.py -m mapping.txt -b Undetermined_S0_L001_I1_001.fastq.gz -f Undetermined_S0_L001_R1_001.fastq.gz -r Undetermined_S0_L001_R2_001.fastq.gz -o demultiplexed

get_observation.py

this script get observation after run split_libraries.py

usage: python get_observation.py

then, the program read all .summary files in the folder and make observation.txt

How to get biggiest gap by abundance

step 1

python get_filenaem.py RefSoilToEMPsoil.out.txt refsoil_filename.txt

step 2

get abundance from summary file

python get_abundance.py

then you will see abundance.txt

step 3

python read_ob_table.py abundance.txt pytable_abun.txt

step 4

python get_final_emp_refsoil.py pytable_abun.txt refsoil_filename.txt emp_final_refsoil_abun.txt not_assigned_abun.txt all_abun.txt

step 5

in excel open not_assigned_abun.txt