qcumber - quality control of genomic sequences

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

qcumber 1.0.1                                     November 2016                                       QCUMBER(1)

       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

       qcumber - quality control of genomic sequences

-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).

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]