platanus¶

Description¶

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.

This module includes the following platanus executables: * Platanus Assembler * Platanus-alle (Platanus2) * Pltanus_trim * MetaPlatanus * BactSNP

Environment Modules¶

Run module spider platanus to find out what environment modules are available for this application.

Environment Variables¶

HPC_PLATANUS_DIR - installation directory
HPC_PLATANUS_BIN - executable directory

Additional Usage Information¶

This module includes the following platanus executables:

Platanus Assembler
Platanus-alle (Platanus2)
Pltanus_trim
MetaPlatanus
BactSNP

Citation¶

If you publish research that uses platanus you have to cite it as follows:

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113.

Categories¶

phylogenetics