focal (1) ccs.1.gz

NAME

       ccs - Generate circular consensus sequences from subreads

SYNOPSIS

       ccs [options] INPUT OUTPUT

DESCRIPTION

       Generate circular consensus sequences (ccs) from subreads.

OPTIONS

       -h,--help
              Output this help.

       --log-level,--logLevel
              Set log level. ["INFO"]

       --version
              Output version info.

       --force
              Overwrite OUTPUT file if present.

       --zmws Generate CCS for the provided comma-separated holenumber ranges only. Default = all

       --maxLength
              Maximum length of subreads to use for generating CCS. [21000]

       --minLength
              Minimum length of subreads to use for generating CCS. [10]

       --minPasses
              Minimum number of subreads required to generate CCS. [3]

       --minPredictedAccuracy
              Minimum predicted accuracy in [0, 1]. [0.9]

       --minIdentity
              Minimum identity to the POA to use a subread. 0 disables this filter. [0.82]

       --minZScore
              Minimum z-score to use a subread. NaN disables this filter. [-3.4]

       --maxDropFraction
              Maximum fraction of subreads that can be dropped before giving up. [0.34]

       --minSnr
              Minimum SNR of input subreads. [3.75]

       --minReadScore
              Minimum read score of input subreads. [0.75]

       --byStrand
              Generate a consensus for each strand.

       --noPolish
              Only output the initial template derived from the POA (faster, less accurate).

       --polish
              Emit high-accuracy CCS sequences polished using the Arrow algorithm

       --polishRepeats
              Polish repeats of 2 to N bases of 3 or more elements. [0]

       --richQVs
              Emit dq, iq, and sq "rich" quality tracks.

       --reportFile
              Where to write the results report. ["ccs_report.txt"]

       --modelPath
              Path to a model file or directory containing model files.

       --modelSpec
              Name of chemistry or model to use, overriding default selection.

       --numThreads
              Number of threads to use, 0 means autodetection. [0]

       --logFile
              Log to a file, instead of STDERR.

       --emit-tool-contract
              Emit tool contract.

       --resolved-tool-contract
              Use args from resolved tool contract.

   Arguments:
       input  Input file.

       output Output file.

AUTHOR

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