SMALT aligns DNA sequencing reads with a reference genome.  


Supported Sequencing Platforms
==============================
Reads from a wide range of sequencing platforms can be processed, for
example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired
reads are supported. There is no support for SOLiD reads.


Strategy
========
The software employs a hash index of short words of up to 20
nucleotides sampled at equidistant steps along the reference genome.
For each sequencing read, potentially matching segments in the
reference genome are identified from seed matches in the index and
subsequently aligned with the read using dynamic programming.


Documentation
=============
http://www.sanger.ac.uk/resources/software/smalt/


Installation
============
./configure
make
make install


Installation on MacOSX (Darwin)
===============================
You might get 32-bit binaries by default with MacOSX Darwin on a 64-bit machine.
In this case use (from version smalt 0.7.4.4)
./configure --build=x86_64-apple-darwin
or
./configure --build=x86_64-apple-darwin --with-bambamc=no


Optional Prerequisites
======================

If you would like to use SAM/BAM as input or BAM as ouput file format,
download and install the bambamc library from GitHub 
https://github.com/gt1/bambamc
Without this library, SMALT expects (possibly gzipped) FASTA/FASTQ
files as input.


Installation with the bambamc library
=====================================

Download the source code for the bambamc library, e.g. as zip file
bambam-master.zip for the library from
https://github.com/gt1/bambamc. To install the bambamc library you
should have the GNU autoconf tools installed
[http://www.gnu.org/software/autoconf].

The installation generates a metadata file bambamc.pc for the
pkg-config tool [http://www.freedesktop.org/wiki/Software/pkg-config]
in the directory $BAMBAMC_INSTALL_DIR/lib/pkgconfig. You may
have to add this directory to the (colon separated) list of paths in
the environment variable PKG_CONFIG_DIR.

The configure script for SMALT uses the pkg-config tool by default to
link the bambamc library. Alternatively, use the ./configure options

./configure --with-bambamc=yes BAMBAMC_CFLAGS="-I$BAMBAMC_INSTALL_DIR/include" BAMBAMC_LIBS="-L$BAMBAMC_INSTALL_DIR/lib -lbambamc"