---
name: "quorum_error_correct_reads"
section: "1"
platform: "linux"
package: "quorum"
version: "1.1.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/quorum_error_correct_reads"
---

# quorum\_error\_correct\_reads(1)

error correct reads from a fastq file based on the k-mer frequencies

## NAME

quorum\_error\_correct\_reads - error correct reads from a fastq file based on the k-mer frequencies

## SYNOPSIS

**error\_correct\_reads** \[*options*\] *db:path sequence:path+*

## DESCRIPTION

Error correct reads from a fastq file based on the k-mer frequencies.

## OPTIONS

default value in (), \*required:

- **-t**, **--thread**=*uint32*

  Number of threads (1)

- **-m**, **--min-count**=*uint32*

  Minimum count for a k-mer to be considered "good" (1)

- **-s**, **--skip**=*uint32*

  Number of bases to skip for start k-mer (1)

- **-g**, **--good**=*uint32*

  Number of good k-mer in a row for anchor (2)

- **-a**, **--anchor-count**=*uint32*

  Minimum count for an anchor k-mer (3)

- **-w**, **--window**=*uint32*

  Size of window (10)

- **-e**, **--error**=*uint32*

  Maximum number of error in a window (3)

- **-o**, **--output**=*prefix*

  Output file prefix (error\_corrected)

- **--contaminant**=*path*

  Jellyfish database of contaminant k-mers

- **--trim-contaminant**

  Trim reads containing contaminated k-mers instead of discarding (false)

- **--homo-trim**=*int32*

  Trim homo-polymer run at the 3' end

- **--gzip**

  Gzip output file (false)

- **-M**, **--no-mmap**

  Do not memory map the input mer database (false)

- **--apriori-error-rate**=*double*

  Probability of a base being an error (0.01)

- **--poisson-threshold**=*double*

  Error probability threshold in Poisson test (1.0e-06)

- **-p**, **--cutoff**=*uint32*

  Poisson cutoff when there are multiple choices

- **-q**, **--qual-cutoff-value**=*uint32*

  Any base above with quality equal or greater is untouched when there are multiple choices

- **-Q**, **--qual-cutoff-char**=*string*

  Any base above with quality equal or greater is untouched when there are multiple choices

- **-d**, **--no-discard**

  Do not discard reads, output a single N (false)

- **-v**, **--verbose**

  Be verbose (false)

- **-U**, **--usage**

  Usage

- **-h**, **--help**

  This message

- **-V**, **--version**

  Version

## AUTHOR

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