Editing BioMicroCenter:IlluminaDataPipeline (section)

=== Software Options ===
While ELAND is extremely fast, it suffers from some significant deficiencies. The largest is the lack of tolerance of errors. Read failure is typically a function of length and it is likely that many nucleotides will have been successfully read before the phasing/pre-phasing or some other error becomes large enough to cause read failure. However, because ELAND is an all or nothing algorithm, it is incapable of handling 'short' reads.  Numerous researchers have made significant efforts to create improved versions of ELAND. Some of the options:

* '''MAQ''' http://maq.sourceforge.net/ -  Maq maps short reads to a reference genome and calls the genotypes from the alignment. It is specificially designed for Illumina-Solexa/AB-SOLiD reads, not for 454 or capillary ones. Key facts about Maq: 1) Maq maps a repeat read randomly, and 2) it gives a probability score (mapping quality) to each alignment. More information is available on the MAQ page.

* '''Bowtie''' - The Burge Lab is currently analyzing the quality of reads mapped using Bowtie. Bowtie is believed to be MUCH faster then ELAND.