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counterr website  

Counterr is a light-weight command line tool that computes errors in sequencing data by comparing the reads to a reference genome. Counterr takes as input an alignment of the reads (bam + bai) and the corresponding reference (fasta) and outputs summaries (figures/tables) of errors in the reads. The tool computes both context independent and context dependent error statistics of the reads. The latter can be particularly helpful for uncovering systematic errors latent in the sequencing technology (due to hardware, basecaller, etc.).

The tool was developed with Oxford Nanopore Technology reads in mind but is general and applicable to other sequencing platforms such as Illumina and PacBio.

Environment Modules

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

System Variables

  • HPC_COUNTERR_DIR - installation directory
  • HPC_COUNTERR_BIN - executable directory