Agalma

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Agalma provides rich diagnostics, including the insert size distribution of paired end data, fraction of reads that are rRNA, and the distribution of sequencing effort across genes. These diagnostics can by summarized as html reports.

Required Modules

Serial

  • gcc/4.7.2
  • agalma

System Variables

  • HPC_AGALMA_DIR - installation directory
  • HPC_AGALMA_BIN - executable directory
  • HPC_AGALMA_DATA - data directory




Citation

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

Dunn CW, Howison M, Zapata F. 2013. Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14(1): 330. doi:10.1186/1471-2105-14-330


Validation

  • Validated 4/5/2018