qcumber - quality control of genomic sequences
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]
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
- -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).
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.