Tepoztlan_ITS

Metabarcodingfungi-milpa. Master project

NATIVE AND HYBRID CORN FUNGUS DIVERSITY ASSESSED THROUGH METABARCODING

AUTHOR: Biol. Olivia Rojo Nava

Contains the scripts to analyse the mycobiome of samples obtained from soil

Programs needed

AMPtk(http://amptk.readthedocs.io/)

Citation

Palmer JM, Jusino MA, Banik MT, Lindner DL. 2018. Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data. PeerJ 6:e4925; DOI 10.7717/peerj.4925.

https://peerj.com/articles/4925/

USEARCH

Trimmomatic

Directory organization

Directory Tepoztlan_ITS/bin has all the scripts (numbered) and the R functions used for data analysis and plotting.

The repository is organized as follows:

| +--bin/
|            +-- 1_quality_check.sh
|            +-- 2_copytepozseqs.sh
|            +-- 3_cleaning.sh
|            +-- 4_amptkillumina.sh

| +--data/
|            +--
| +--figures/
|            +--

1. Script 1_quality_check.sh

Performs the fastQC analysis in each sample

2. Script 2_copytepozseqs.sh

Copy all the Raw sequences with .gz extension from /data/raw/run-144833689 to the folder tepoz located in ../data/tepoz/

3. Script 3_cleaning.sh

This script cleans the sequences R1 & R2 using Trimmomatic and the Option SLIDINGWINDOW

The output are several files with extension fastq.gz which will be then used to complete the fastQC analysis

4. Script 4_amptkillumina.sh

Analyse mycobiome for NGS dataprocess demultiplexed Illumina MiSeq 2x300 read, using the amptk pipeline