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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

python 2.7.3, fastqc 0.10.1, oases 0.2.08, samtools 0.1.18, trinity r20120608, velvet 1.2.07, ncbi_blast 2.2.26, bowtie 2.0.0b6


  • Agalma

Parallel (OpenMP)

  • intel
  • Agalma

Parallel (MPI)

  • intel
  • openmpi
  • Agalma

System Variables

  • HPC_{{#uppercase:Agalma}}_DIR - installation directory