.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH QCUMBER "1" "November 2016" "qcumber 1.0.1" "User Commands"
.SH NAME
qcumber \- quality control of genomic sequences
.SH SYNOPSIS
.B qcumber
 [\-h] [\-input INPUT] [\-1 R1] [\-2 R2] [\-output OUTPUT]
\fB\-technology\fR {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]
.SH DESCRIPTION
QCPipeline is a tool for quality control. The workflow is as follows:
.nr step 1 1
.IP \n[step] 3
Quality control with FastQC
.IP \n+[step]
Trim Reads with Trimmomatic
.IP \n+[step]
Quality control of trimmed reads with FastQC
.IP \n+[step]
Map reads against reference using bowtie2
.IP \n+[step]
Classify reads with Kraken
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-input\fR INPUT
input sample folder. Illumina filenames have to end
with _<lane>_<R1|R2>_number, e.g.
Sample_12_345_R1_001.fastq
.TP
\fB\-1\fR R1
input file. Illumina filename must not match
<project>_<lane>_<R1|R2>_<number> name pattern
.TP
\fB\-2\fR R2
input file
.HP
\fB\-output\fR OUTPUT
.HP
\fB\-technology\fR {Illumina,IonTorrent}
.HP
\fB\-threads\fR THREADS
.HP
\fB\-adapter\fR {TruSeq2\-PE,TruSeq2\-SE,TruSeq3\-PE,TruSeq3\-SE,TruSeq3\-PE\-2,NexteraPE\-PE}
.TP
\fB\-reference\fR REFERENCE
Map reads against reference
.TP
\fB\-index\fR INDEX
Bowtie2 index if available.
.TP
\fB\-sav\fR SAV
Illumina folder for SAV. Requires RunInfo.xml,
RunParamter.xml and Interop folder.
.HP
\fB\-save_mapping\fR
.TP
\fB\-db\fR DB
Kraken database
.TP
\fB\-palindrome\fR PALINDROME
Use palindrome parameter 30 or 1000 for further
analysis. Default:30
.TP
\fB\-minlen\fR MINLEN
Minlen parameter for Trimmomatic. Default:50
.TP
\fB\-trimOption\fR TRIMOPTION
Use maxinfo or slidinginfo for
Trimmomatic.MAXINFO:<target length>:<strictness> |
SLIDINGWINDOW:<window size>:<required quality>.
default: SLIDINGWINDOW:4:15
.TP
\fB\-version\fR
show program's version number and exit
.HP
\fB\-nokraken\fR
.HP
\fB\-nomapping\fR
.TP
\fB\-trimBetter\fR
Optimize trimming parameter using 'Per sequence base
content' from fastqc. Not recommended for amplicons.
.TP
\fB\-trimBetter_threshold\fR TRIMBETTER_THRESHOLD
Set \fB\-trimBetter\fR to use this option.Default setting for
Illumina: 0.15 and for IonTorrent: 0.25.
.TP
\fB\-forAssembly\fR
Set \fB\-trimBetter\fR to use this option.Trim parameter are
optimized for assemblies (trim more aggressive).
.TP
\fB\-forMapping\fR
Set \fB\-trimBetter\fR to use this option.Trim parameter are
optimized for mapping (allow more errors).
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.