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phyloflash website  

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.

Environment Modules

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

System Variables

  • HPC_PHYLOFLASH_DIR - installation directory
  • HPC_PHYLOFLASH_BIN - executable directory


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

Harald R Gruber-Vodicka, Brandon KB Seah, Elmar Pruesse. phyloFlash — Rapid SSU rRNA profiling and targeted assembly from metagenomes.