Here are the papers that describe ALLPATHS-LG:

Gnerre S, MacCallum I, Przybylski D, Ribeiro F, Burton J, Walker B, Sharpe T, Hall G, Shea T, Sykes S, Berlin A, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. High-quality draft assemblies of mammalian genomes from massively parallel sequence data Proceedings of the National Academy of Sciences USA (January 2011 vol. 108 no. 4 1513-1518).

Ribeiro F, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, MacCallum I, Nusbaum C, Jaffe DB.  Finished bacterial genomes from shotgun sequence data. Genome Research 22: 2270–7.

Here are the papers that describe its predecessor, ALLPATHS:

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research 18: 810–20.

MacCallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB. 2009. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biology 10: R103.

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