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Bioinformatics tools

In addition to workflows, EPI2ME maintains a small set of standalone tools that can be used to perform specific tasks. These tools are designed to be easy to use and integrate into your existing workflows. The mostly perform basic tasks such as file format conversion, data manipulation, and quality control. Their development is driven by functionality required in our workflows.

Available tools

  • fastcat - a tool to concatenate FASTQ files, demultiplex files, and calculate summary statistics. Also provides statistics for BAM files. [Github]
  • percula - a preprocessor to take spatial single-cell data output from Oxford Nanopore Technologies' sequencing devices into 10X Genomics' Space Ranger.
  • ezcharts - a plotting library that simplifies the creation of interactive reports from bioinformatics file. [Github]
  • kraken2-server - a server for running Kraken2 taxonomic classification on large datasets. [Github]
  • pore-c-py - standalone processing of Pore-C chromatin capture sequencing data, outside wf-pore-c. [Github]