Counterr¶

Description¶

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.).

Environment Modules¶

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

Environment Variables¶

HPC_COUNTERR_DIR - installation directory
HPC_COUNTERR_BIN - executable directory

Categories¶

phylogenetics