---
name: "qcumber"
section: "1"
platform: "linux"
package: "qcumber"
version: "2.3.0-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/qcumber"
---

# qcumber(1)

quality control of genomic sequences

## NAME

qcumber - quality control of genomic sequences

## SYNOPSIS

**qcumber**\
  \[-h\] \[-input INPUT\] \[-1 R1\] \[-2 R2\] \[-output OUTPUT\] **-technology** {Illumina,IonTorrent} \[-threads THREADS\] \[-adapter {TruSeq2-PE,TruSeq2-SE,TruSeq3-PE,TruSeq3-SE,TruSeq3-PE-2,NexteraPE-PE}\] \[-reference REFERENCE\] \[-index INDEX\] \[-sav SAV\] \[-save\_mapping\] \[-db DB\] \[-palindrome PALINDROME\] \[-minlen MINLEN\] \[-trimOption TRIMOPTION\] \[-version\] \[-nokraken\] \[-nomapping\] \[-trimBetter\] \[-trimBetter\_threshold TRIMBETTER\_THRESHOLD\] \[-forAssembly\] \[-forMapping\]

## DESCRIPTION

QCPipeline is a tool for quality control. The workflow is as follows:

- 1

  Quality control with FastQC

- 2

  Trim Reads with Trimmomatic

- 3

  Quality control of trimmed reads with FastQC

- 4

  Map reads against reference using bowtie2

- 5

  Classify reads with Kraken

## OPTIONS

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

  show this help message and exit

- **-input** INPUT

  input sample folder. Illumina filenames have to end with \_\<lane\>\_\<R1\|R2\>\_number, e.g. Sample\_12\_345\_R1\_001.fastq

- **-1** R1

  input file. Illumina filename must not match \<project\>\_\<lane\>\_\<R1\|R2\>\_\<number\> name pattern

- **-2** R2

  input file

**-output** OUTPUT

**-technology** {Illumina,IonTorrent}

**-threads** THREADS

**-adapter** {TruSeq2-PE,TruSeq2-SE,TruSeq3-PE,TruSeq3-SE,TruSeq3-PE-2,NexteraPE-PE}

- **-reference** REFERENCE

  Map reads against reference

- **-index** INDEX

  Bowtie2 index if available.

- **-sav** SAV

  Illumina folder for SAV. Requires RunInfo.xml, RunParamter.xml and Interop folder.

**-save\_mapping**

- **-db** DB

  Kraken database

- **-palindrome** PALINDROME

  Use palindrome parameter 30 or 1000 for further analysis. Default:30

- **-minlen** MINLEN

  Minlen parameter for Trimmomatic. Default:50

- **-trimOption** TRIMOPTION

  Use maxinfo or slidinginfo for Trimmomatic.MAXINFO:\<target length\>:\<strictness\> \| SLIDINGWINDOW:\<window size\>:\<required quality\>. default: SLIDINGWINDOW:4:15

- **-version**

  show program's version number and exit

**-nokraken**

**-nomapping**

- **-trimBetter**

  Optimize trimming parameter using 'Per sequence base content' from fastqc. Not recommended for amplicons.

- **-trimBetter\_threshold** TRIMBETTER\_THRESHOLD

  Set **-trimBetter** to use this option.Default setting for Illumina: 0.15 and for IonTorrent: 0.25.

- **-forAssembly**

  Set **-trimBetter** to use this option.Trim parameter are optimized for assemblies (trim more aggressive).

- **-forMapping**

  Set **-trimBetter** to use this option.Trim parameter are optimized for mapping (allow more errors).

## AUTHOR

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