QCUMBER(1)

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:

    Quality control with FastQC

    Trim Reads with Trimmomatic

    Quality control of trimmed reads with FastQC

    Map reads against reference using bowtie2

    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.