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.