SeqAlto is an aligner specifically designed for Illumina reads of length greater or equal to about 100-bp. It takes advantage of this longer read length to provide fast alignment rates and accurate placement of polymorphic reads. Paired-end reads are recommended for even greater accuracy. When aligning 100-bp paired-end reads SeqAlto is on average about 2-4x faster than BWA while being more sensitive and much faster for longer reads.
- MacOsX/ Linux
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John C. Mu, Hui Jiang, Amirhossein Kiani, Marghoob Mohiyuddin, Narges Bani Asadi and Wing H. Wong,
Fast and Accurate Read Alignment for Resequencing,
Bioinformatics (2012) 28 (18): 2366-2373.