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.