qcumber1

Quality control of genomic sequences

Usage

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]

Overview

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).

Releases

Unchanged in 4 releases since Debian 10 (Buster).

10–13