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#Hardware/Software Requirements - 64 bit Linux or Mac OS X - x86-64 compatible processors

#Tutorial https://github.com/Juassis/iedb PDF

RELEASEnotes contains detailed information about the latest major release

#Directory Contents main dir

	assis.pl, params_model

bin: scripts

 compare_orthogroups_by_synteny.pl, export_rnaseq.pl, fix_gff_from_bedtools.sh, gene_overlap_report.pl, gff2fasta.pl, overlap_gff.pl, protein_check.pl, protein_coding_report.pl, rnaseq_report.pl

tests: DataSet Example

D_simulans_Assessment

	FASTA: Drosophila_simulans.fasta, Drosophila_melanogaster.fasta
	GFF:   Drosophila_simulans.gff3, Drosophila_melanogaster.gff3

	OUTPUT:
		PROTEINS: Drosophila_simulans_proteins.fasta
		REPORT: report_overlap, report_protein_coding

doc: documentation

Tutorial:PDF
Paper: Link

#Installation

 Interpreters: Perl, Python

• Perl
  • Libraries
    • BioPerl (current version)

• Python 2.7

  • Libraries

    • Numpy (python 2.7)

Install dependencies: OrthoFinder, BedTools

####OrthoFinder:

• Tutorial

Installation - Latest Development Version

• MAC: - Install the source package

All SO

• Install dependencies: MCL, FASTME and DIAMOND or MMseqs2

• Install the source package if some of the dependencies do not work

####BedTools

Installation - Latest Version

• MAC: brew install bedtools

• Linux: apt-get install bedtools

ASSIS Software Installation

##ASSIS

# Get latest ASSIS releases from github

wget https://github.com/Juassis.tar.gz
tar -xzf XXX.tar.gz
cd ASSIS

# Alternatively, get ASSIS using git

git clone https://github.com/Juassis/iedb.git

Running the program:

To Run ASSIS use the Example DataSet:

Project/
	bin
	params_model
	assis.pl
	D_simulans_Assessment
	README.md
	Tutorial.md

	1- cd D_simulans_Assessment		

		FASTA/ Drosophila_simulans.fasta, Drosophila_melanogaster.fasta
		GFF/  Drosophila_simulans.gff3, Drosophila_melanogaster.gff3
		OUTPUT/

	2- perl assis.pl -d D_simulans_Assessment -p params_model

Running with the own DataSet:

Command Line and Options:

1- mkdir Project

2- cd Project

	3- mkdir FASTA
		3.1 ln -s genome.fasta (Evaluated and Reference (Closely related species)) FASTA;

	4- mkdir GFF
		4.1 ln -s genome.gff (Evaluated and Reference) GFF;

		* FASTA and GFF should have the same suffix (See Example DataSet for fruit fly genome); *

	 	4.2 This Only for RNASeq Mapped Data (See the tutorial to generate a bam/bed file)


5- Edit the params file (see the tutorial)

6- mkdir OUTPUT

7- perl bin/Assis.pl -d Project -p params_model

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###Limitations

Splicing leader/ Trans splicing

Fragmented genomes (Finished genomes annotation to help)

This release was tested with the default parameters for drosophila, mouse and parasites genomes. Mammal genomes require at least 4GB of RAM, ideally 16GB.