MAPS is short for "MEGAPRIMER Amplicon Processing System" and is a analysis pipeline for Mimiviridae polB gene amplicon analysis generated with next gen sequencing systems (e.g. Illumina MiSeq).
The first version (i.e. MAPS) was published by Li & Hingamp et al. (2018) and was mostly based on bash and python. The current version was built on R, bash and python and incorporates dada2 (Callahan et al. 2016).
MAPS2 can be used with and without the qsub system. However other software and applications are necessary:
- R/3.6.1
- dada2
- seqinr
- RcppParallel
- ggtree
- treeio
- Python/3.7.5
- Bio
- random
- re
- blast+/2.9.0
- pplacer/1.1.alpha19
- mafft/7.453
- cd-hit/4.6.1
MAPS2 is run by executing the main script called MAPS2_main_pipeline.tcsh. This script will call other tcsh, python and R scripts. It is necessary to defining three variables in the pipeline by opening the main script and edditing the following three variables:
-
The output of the pipeline will be stored in the directory assigned to:
MAIN_DIR. -
A directory holding the MEGAPRIMER amplicon sequencing fastq input files (zipped also okay). The absolute path must be assigned to:
R_path_to_raw. -
Finally, MAPS2 needs to be told were scripts and references are located:
MAPS2_DIR. All necessary scripts and references can be downloaded here.
- The script called at first uses dada2 in R. This script does most of the work.
- blastx on the ASVs to check if they are viral sequences. (saves translated amino acid sequences).
- a bash command (sed...) to make a fasta file from the blast output.
- mafft adds Mimiviridae ASVs sequences to a reference file.
- pplacer places the ASVs in a reference tree (Endo et al. 2020).
- Another R script removes ASV that were not placed within the Mimiviridae branch (saves a statistics table).
- All ASVs are trimmed in a common region (common region hardcoded in this pipeline).
- Clustering trimmed ASVs at 100% (99%, 97%) nucleotide indentity
- Creating a final ASV table from clustered ASVs.