BWA aligner

The BWA aligner for short read alignment is by Heng Li and Richard Durbin.

BWA mem
On the BWA website, it explains the the 'bwa mem' algorithm is the best one for '70bp or longer Illumina, 454, Ion Torrent and Sanger reads, assembly contigs and BAC sequences.'

I've previously used it something like this:
bwa mem genome.fasta reads_fastq.gz mates_fastq.gz | samtools view -b -S -F 4 - > output.bam
   run 'bwa mem' to align reads and their mates to a genome, and pipe the output through samtools to just take the reads that align (using -F4) and discarding reads that don't align (to save disk space), and put the output in output.bam

Other options
Other options available in BWA include:
bwa sampe: generated paired ended alignments (This takes an option -a <max_insert_size>)