ALLPATHS-LG

ALLPATHS-LG

 

ALLPATHS-LG is a short read assembler.  It is developed and supported by the Broad Institute.

Documentation

• ALLPATHS-LG web site
• Publications:
  • 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.

 

Usage

To see what versions of ALLPATHS-LG are available type

module avail allpaths-lg

To see what other modules are needed, what commands are available and how to get additional help type

module help allpaths-lg

To use ALLPATHS-LG, include a command like this in your batch script or interactive session to load the ALLPATHS-LG module:

module load allpaths-lg

Be sure you also load any other modules needed, as listed by the module help allpaths-lg command.