NAME

       EstimateError.py - Calculates annotation set error rates

DESCRIPTION

       usage: EstimateError.py [--version] [-h]  ...

       Calculates annotation set error rates

   help:
       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

   subcommands:
              Estimation method

       set    Estimates error statistics within annotation sets.

       barcode
              Calculates pairwise distance metrics of barcode sequences.

   output files:
              error-position

              estimated error by read position.

              error-quality

              estimated error by the quality score assigned within the input file.

              error-nucleotide

              estimated error by nucleotide.

              error-set

              estimated error by annotation set size.

              distance-set

              pairwise hamming distances by annotation set.

              threshold-set

              thresholds from pairwise hamming distances for annotation sets.

              distance-barcode

              estimated error by pairwise hamming distances

              threshold-barcode

              thresholds from pairwise hamming distances for clustering barcodes

   output fields:
              POSITION

              read position with base zero indexing.

              Q

              Phred quality score.

              OBSERVED

              observed nucleotide value.

              REFERENCE

              consensus nucleotide for the barcode read group.

              SET_COUNT

              barcode read group size.

              REPORTED_Q

              mean  Phred  quality  score  reported within the input file for the given position, quality score,
              nucleotide or read group.

              MISMATCHES

              count of observed mismatches from consensus for the given position, quality score,  nucleotide  or
              read group.

              OBSERVATIONS

              total count of observed values for each position, quality score, nucleotide or read group size.

              ERROR

              estimated error rate.

              EMPIRICAL_Q

              estimated error rate converted to a Phred quality score.

              ALL

              histogram (count) of all pairwise distance distribution.

              DTN

              histogram (count) of distance to nearest distribution.

              DISTANCE

              length normalized hamming distance.

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

EstimateError.py 0.6.0                              May 2020                                 ESTIMATEERROR.PY(1)