The BWA aligner for short read alignment is by Heng Li and Richard Durbin.
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 available in BWA include:
bwa sampe: generated paired ended alignments (This takes an option -a <max_insert_size>)