---
name: "ccs"
section: "1"
platform: "linux"
package: "unanimity"
version: "3.3.0+dfsg-2.1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/ccs"
---

# ccs(1)

Generate circular consensus sequences from subreads

## 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.