Installation
--------------
The installation is quite straightforward. Uncompress the tar ball, enter the 'src' subdirectory and then issue the following command if you are installing it on a Linux/unix computer:

make -f Makefile.Linux

or issue the following command if you are installing it on a Mac OS X computer:

make -f Makefile.MacOS

Subread also supports FreeBSD and OpenSolaris/Oracle Solaris. Please note that both FreeBSD and Solaris do not use GNU make as the default make program, hence you need to use gmake instead of make to build the subread package:

gmake -f Makefile.FreeBSD

or

gmake -f Makefile.SunOS

A new subdirectory 'bin' will be created under the home directory of this software package, and the executables generated from the compilation will be saved to it.

To enable easy access to these executables, you may copy the executables to a system directory such as '/usr/bin' or add the path to the executables to your search path (modify the environment variable `PATH').

A Quick Start
--------------
An index should be built before carrying out read alignments: 

subread-buildindex -o my_index chr1.fa chr2.fa ...
(You may provide a single FASTA file including all chromosomal sequences).

With built index, you can now align reads to the reference genome. Align single-end reads: 

subread-align -i my_index -r reads.txt -o subread_results.sam

Align paired-end reads:

subread-align -i my_index -r reads1.txt -R reads2.txt -o subread_results_PE.sam

Detect exon-exon junctions from RNA-seq data (read mapping results are also generated):

subjunc -i my_index -r reads1.txt -R reads2.txt -o subjunc_results.sam

Assign mapped reads to genomic features (eg. genes):

featureCounts -a annotation.gtf -o counts.txt subread_results.sam

Tutorials
-------------------
A short tutorial for Subread - http://bioinf.wehi.edu.au/subread
A short tutorial for Subjunc - http://bioinf.wehi.edu.au/subjunc
A short tutorial for featureCounts - http://bioinf.wehi.edu.au/featureCounts

Users Guide
--------------
Users Guide can be found in the 'doc' subdirectory. It provides comprehensive descriptions to the programs included in this package.

Citation
--------------
If you use Subread or Subjunc aligners, please cite:

Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013

If you use the featureCounts program, please cite:

Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 2013. doi: 10.1093/bioinformatics/btt656

Get help
--------------
You may subscribe to the SeqAnswer forum (http://www.seqanswers.com) or the Bioconductor mailing list (http://bioconductor.org/) to get help. Alternatively, you may directly contact Wei Shi (shi at wehi dot edu dot au) or Yang Liao (liao at wehi dot edu dot au) for help.
