Free Software Applications

Qiime Bash Script

This Bash script was created for Qiime 1 users. If you are interested in using Qiime2, please use the FASTq processor. The downloaded bash script will prompt the user through three Qiime scripts:


    1. This script joins the foward read (R1) and reverse read (R2)  fastq files. These fastq files are the raw fastq files downloaded from basespace and are untouched.
    1. This script formats the join.fastq to be compatible with
    2. The user will use the output from the script; default=fastqjoin.join.fastq.
    3. The user will also need a properly formatted mapping file to remove the barcodes. If you are working with MRDNA data, this mapping file will be found in the fasta-qual-mapping-files folder that you received (ProjectID-mapping.txt).
      1. If you are NOT using MRDNA data, be aware that the barcode length is set to 8. If this is not the case for your data, you will need to update the --bc1_len and --bc2_len options accordingly.
    1. This script will demultiplex your illumina data and create the seqs.fna file
    2. The user will need the output from the; default= reads.fastq and barcodes.fastq
    3. The user will also need the same mapping file as used for
    4. Lastly, the user can specifiy the quality threshold they would like to use to filter the sequences. The qiime default value is 19


This script should be downloaded onto the same computer where the Qiime application was installed. Each script can be run from the terminal (command line) using the ./bashscriptname command.


Once the seqs.fna file has been generated, the user can continue on with the illumina overview tutorial found on Qiime website. The next script in the tutorial is -i seqs.fna

Qiime Bash Script