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 German Tischler's BAMBAM library from
ftp://ftp.sanger.ac.uk/pub/users/gt1/

Without this library, SMALT expects (possibly gzipped) FASTA/FASTQ
files as input.
