EMAGC

Eukaryotic Metagenome-Assembled Genome - Gene Calling

Description

It predicts genes from Eukaryotic MAGs.

• It first trains Augustus through BUSCO
• Then, it predicts genes from contigs longer than a specific size (defined by the user) using Augustus in the MAKER pipeline.
• The resulting genes are used to train SNAP through MAKER.
• After SNAP training, genes are called from all contigs using SNAP and AUGUSTUS in MAKER.
• The predicted proteins are then annotated against the Pfam database.

A comprehensive documentation for EMAGC is hosted on readthedocs

Installation

Clone the repository from GitHub:

git clone https://github.com/lfdelzam/EMAGC

This directory contains the scripts:

 EMAGCpoly.sh
 EMAGCsingle.sh

Usage

One MAG

bash EMAGCsingle.sh [options]:

-m=<absolute path to mag file>
-s=<min contig size for SNAP training, default=5000>
-p=<threads>
-b=<conda or module,busco environment or package name, e.g -b="conda,busco_env">
-k=<conda or module,MAKER environment or package name, e.g., -k="conda,maker_env">
-a=<conda or module,hmmer environment or package name, e.g., -a="conda,annot_env", default -a=skip>
-l=<busco lineage (e.g., eukaryota_odb10) or auto, default=eukaryota_odb10>
-n=<number of SNAP training, default=1>
-u=<absolute path to protein db or none, default=none>
-r=<absolute path to cDNA sequence file in fasta format from an alternate organism or none, default=none>
-w=<absolute path to Pfam hmm database or none, default=none>
-v=<E-value threshold used during Pfam annotation, e.g., -v='-E 0.001', default='--cut_ga'>
-q=<remove all temporary files, y for yes or n for no, default=no>

Several MAGs

bash EMAGCpoly.sh [options]:

-D=<path to mag directory>
-E=<MAG extention, default ".fa">
-S=<min contig size for SNAP training, default=5000>
-P=<threads>
-B=<conda or module,busco environment or package name, e.g., -B="conda,busco_env">
-K=<conda or module,MAKER environment or package name, e.g., -K="module,maker">
-A=<conda or module,hmmer environment or package name, e.g., -A="conda,annot", default -A=skip>
-L=<busco lineage (e.g., eukaryota_odb10) or auto, default=eukaryota_odb10>
-N=<number of SNAP training, default=1>
-U=<absolute path to protein db or none, default=none>
-R=<absolute path to cDNA sequence file in fasta format from an alternate organism or none, default=none>
-W=<absolute path to Pfam hmm database or none, default=none>
-V=<E-value threshold used during Pfam annotation, e.g., -V='-E 0.001', default='--cut_ga'>
-Q=<remove all temporary files, y for yes or n for no, default=no>
-F=<Force the re-execution, yes or no, default=no>