File	Date	Author	Commit
Src	2016-02-24	yye	[c6e112] intial commit to sourceforge
README	2015-04-07	Yuzhen Ye	[cf4212] fix README

Read Me

Program Name: TAG (transcript assembly by mapping reads to graphs)
Version: 0.91
Released on Jan 22, 2015
Developer: Yuzhen Ye <yye@indiana.edu> and Haixu Tang <hatang@indiana.edu>
Affiliation: School of Informatics and Computing, Indiana University, Bloomington

The development of TAG was supported by NIH grant: NIH 1R01AI108888-01A1

TAG is free software under the terms of the GNU General Public License as published by 
the Free Software Foundation.

>> Introduction

TAG is a tool for metatranscriptome assemby by mapping metatranscriptomic reads onto graphs of matched metagenome assembly. 

TAG on the web: http://omics.informatics.indiana.edu/TAG
  (Please check the project home page for updates and newer version of the program)

>> Installation

go to Src/ (the source file folder), then call:
make clean
make

The executable file "tag" will be created under the same folder

>> Dependents
TAG itself does not rely on any third party software; but it takes outputs from other software as its inputs.
1) SOAPdenovo2 (or SOAPdenovo); it is required for assembling matched metagenome, generating both *.contig and *.edge files.
   SOAPdenovo2 is available at http://sourceforge.net/projects/soapdenovo2/.
2) Bowtie2; it is required for aligning metatranscriptomic datasets onto metagenome assembly (the contig file), providing the sam file
   Bowtie2 is availalbe at http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

>> Using tag 

Usage: type tag for usages
Inputs:
    metatranscriptomic sequences (strand-specific reads, in fasta format or fastq format)
    assembly of matched metagenome (*.contig and *.edge files)
    alignment of the metatranscriptomic reads onto the linear contigs in SAM format 

Example usage: ./tag -i T.1.fa -j T.2.fa -e G.edge -s G.contig -m S.sam -k 31 -o test-tag

Inputs:
    T.1.fa & T.2.fa  -- metatranscriptomic datasets
    G.edge & G.contig -- the assembly of matched metagenome (the graph file & the sequence file of the contig), produced by SOAPdenovo2
    31 -- the k-mer size (NOTE: the k-mer must be same as the one used in the SOAPdenovo2 assembly!!)
    S.sam -- the alignment of T.1.fq & T.2.fq against G.contig, derived by Bowtie 2
Outputs:
    test-tag.fa -- assembled transcripts
    test-tag.vertex & test-tag.edge -- other outputs regarding the transcript graph (for more advanced uses, use -y option)

>> Test datasets
Check out datasets for testing the software at the TAG website