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.

AUTHOR¶

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