___                       ______  _     _             
   / __)             _       (_____ \| |   (_)            
 _| |__ _____  ___ _| |_ ____  ____) ) |__  _  ___  ____  
(_   __|____ |/___|_   _) _  |/ ____/|  _ \| |/ _ \|    \ 
  | |  / ___ |___ | | || |_| | (_____| |_) ) | |_| | | | |
  |_|  \_____(___/   \__)__  |_______)____/|_|\___/|_|_|_|
                           |_|                            

• NOTE fastq2biom is no longer being maintained as I have migrated towards ASV-based approach with data2.

fastq2biom

PE Illumina FASTQ to biom superscript

A draft Z shell script automating steps processing Illumina paired-end FASTQ to a BIOM format. Developed for Z-shell (zsh).

What's new?

1. ITS (usearch9) support added.
2. 16S (usearch10) support added.
3. 16S relaxed merge mode added.
4. In usearch10, unoise3 support and updated codes added.

To use:

• Place all and only the paired-end Illumina files of the this project in this local folder.
• The ID of the sample in the file name should be deliminted by underscore; e.g. "SampleID_L001_R1.fastq".
• I used Anaconda conda create -n python2 python=2.7 anaconda to create a Python 2 envrionment which is activated via source activate python2 in the script. If you're not natively in Python 3, you can probably comment out the lines (starting with source) that activate and deactivates the environment.

Dependencies:

The following commands need to be in the $PATH variable, and named as such:

• mothur - from http://www.mothur.org
• biom - from http://biom-format.org
• usearch[n] - from http://www.drive5.com (Note the version-dependent scripts)
• Optional QIIME scripts

TODO:

• Generate FASTQC report of the input FASTQ files.
• fastx_learn error rate determination.
• Report sequence size distribution (gist: cyklee/fastx_sequence_length.sh).
• Report pre-processing read counts (simple grep for unfiltered fastq).
• Testing 16S_usearch10 script for unoise3 and singleton inclusion (alpha=Y).

Possibly?

• Snakemake?
• Perhaps use the size distribution to calculate trim.seq parameters (e.g. adjust to capture a portion of the distribution).

Issues

• Previous log file issue solved due to logging being supported by newer usearch.