Metabarcoding Multiprimer approach pipeline for sequences from Illumina platform #MMAP Metabarcoding Multiprimer approach pipeline for Illumina platform - by Iván Batuecas-
MMAP is a metabarcoding pipeline used to sequences obtained from illumina platform used to study the gut content from predator insect (https://biorxiv.org/cgi/content/short/2021.05.19.444782v1). The pipile is integrating by different functions from , VSEARCH, BIOPYTHON, CUTADAPT and other programs.
The pipeline is run as Bash that automatically generates the output in differents folders and the logfile from each execute script that contain a complete output from the console.
For a a short tutorial on analysed sequences from metabarcoding datasets obtained from https://biorxiv.org/cgi/content/short/2021.05.19.444782v1
If you like BASTA and use it for publications please cite it as "Kahlke T and Ralph PJ (2018), BASTA–Taxonomic classification of sequences and sequence bins using Last Common Ancestor estimations. Meth. Ecol. Evol. doi:10.1111/2041‐210X.13095"
About MMAP Please keep in mind that MMAP needs differnt software (Vsearch , Cutadapt...) installed to work properly. For it, the best way is the use of two Anaconda enviroment. The pipeline was tested in Linux based systems (Ubuntu 20.04 LTS), so I recommend strongly its use in this operating systmem.
To install MMAP locally Install Anaconda https://docs.anaconda.com/anaconda/install/
-Select your own operating systems (linux Ubuntu 20.04, in my case)
-We have to create a two diffent enviroments: conda create -n Env_1 python=3.6;
conda create -n Env_2 python=2.7
git clone https://github.com/Ivanbh214/MMAP
conda activate Env_1
./Requeriments_python_3.sh
conda activate Env_2
./Requeriments_python_2.sh
-Adjust the parameters in the scritps to the need of your experiments, by default is included the parameters used in https://biorxiv.org/cgi/content/short/2021.05.19.444782v1 (for it, see the tools description).
In script_1: -Fix the working directory -Fix the merged parameters -Number of samples -Number of primers for the split
In script_2: -Fix similarity % for the clustering -Fix the chimera algorith detection -Fix the blast parameters
In script_3 -Fix the LCA algoriths parameters
-Execute the script in secuential order firstly for the samples amplified with arthorpod primers and the for plant samples:
conda activate Env_1
./Script_1_Art.sh
./Script_2_Art.sh
conda deactivate Env_1
conda activate Env_2
./Script_3_Art.sh