Glint

Glint is a general purpose nucleic acid sequence aligner.

It is is based on a seed-and-extend alignment approach.
The glint sofwtare is extensively used by the Narcisse genome browser (http://narcisse.toulouse.inra.fr, [1])

Initially designed to compare large genomes it handles now different alignment
process:

• aligning large chromosomes of genomes
• aligning a genome against itself
• aligning a set of reads against a genome
• aligning a set of paired-end reads against a genome

In addition, glint encapsulates a conversion utility between a large number of formats (fastq, fasta, bam, sam, bed)

The software can be downloaded from the "Files" tab

[1] Courcelle E, Beausse Y, Letort S, Stahl O, Fremez R, Ngom-Bru C, Gouzy J and Faraut T (2008) Narcisse: a mirror view of conserved syntenies. NAR 36:D485-90.