update readme

schellt · Oct 14, 2019 · 151f1de · 151f1de
1 parent 05672a3
commit 151f1de
Showing 1 changed file with 47 additions and 50 deletions.
diff --git a/readme.md b/readme.md
@@ -6,20 +6,17 @@ Waldvogel A-M, Schell T
 ## Description
 __Trimming (overrepresented *k*-mers from) multiple fastq files.__
 
-After each trimming a test for overrepresented *k*-mers will be executed, if not switched off. Any overrepresented *k*-mers found will be added to a global list and the trimming will be repeated on the original input files together with the overrepesented *k*-mers until no overrepresentation is detected.
-
-Autotrim uses Trimmomatic for trimming, FastQC for overrepresentaion screening and MultiQC to generate summary reports.
-The dependencies will be automatically detected if `java`, `trimmomatic`, `fastqc` or `multiqc` is in your `$PATH`. Execution of MultiQC is optionally and will be skipped if not found in your `$PATH` and `-mqcp` is not specified.
-
+After each trimming a test for overrepresented *k*-mers will be executed, if not switched off. Any overrepresented *k*-mers found will be added to a global list and the trimming will be repeated on the original input files together with the overrepesented *k*-mers until no overrepresentation is detected.  
+Autotrim uses Trimmomatic for trimming, FastQC for overrepresentaion screening and MultiQC to generate summary reports.  
+The dependencies will be automatically detected if `java`, `trimmomatic`, `fastqc` or `multiqc` is in your `$PATH`. Execution of MultiQC is optionally and will be skipped if not found in your `$PATH` and `-mqcp` is not specified.  
 Autotrim distinguishes automatically between paired and single end data.
 
 ## Dependencies
-
-- Trimmomatic: [http://www.usadellab.org/cms/?page=trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)
-- FastQC: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 __Optional__
-- MultiQC: [http://multiqc.info/](http://multiqc.info/)
+- [MultiQC](http://multiqc.info/)
 
 ## Usage
 ### Prerequisites
@@ -37,49 +34,46 @@ __While choosing a root direcory will skip the subdirectory when it contains mor
 
 ### Output
 Fastq output files are created in the same directory as the corrensponding input file.
-The `.f(ast)q(.gz)` file extension will be removed and `_autotrim.fq` for single end data and `_autotrim.paired.fq` and `_autotrim.unpaired.fq` will be added to the end of the file name respectively.
-
-FastQC reports will be created for single end input data and the paired output fastq files for paired end input (not for the unpaired output).
-
-Standard out `*.trimmomatic_log` and standard error `*.trimmomatic_err` from each Trimmomatic run will be saved in the same folder as the input.
-
+The `.f(ast)q(.gz)` file extension will be removed and `_autotrim.fq` for single end data and `_autotrim.paired.fq` and `_autotrim.unpaired.fq` will be added to the end of the file name respectively.  
+FastQC reports will be created for single end input data and the paired output fastq files for paired end input (not for the unpaired output).  
+Standard out `*.trimmomatic_log` and standard error `*.trimmomatic_err` from each Trimmomatic run will be saved in the same folder as the input.  
 The MultiQC report will be placed either in the root directory if `-d` is used or in the directory of the log and overrepresented *k*-mers files if `-fofn` is used.
+
 ```
 autotrim.pl [-d <root_dir> | -fofn <file_of_file_names> -log <dir_to_place_the_log-file>]
             -to <trimmomatic_options> -trim <trimmomatic_trimmer>
-```
 
-__Options: [default]__
-
-```
--d STR          Root directory for automatic input of multiple data sets. The file containing overrepresented
-                k-mers (kmer.fa) and the autotrim log file (autotrim.log) will be saved in this directory.
--fofn STR       File of file names containing tab-seperated paths to one data set per line.
--log STR        Specify the path to save the file containing overrepresented k-mers (kmer.fa) and the log
-                file of autotrim (autotrim.log) if using -fofn.
--to STR         A file containing Trimmomatic options that should be used. All options need to be in the
-                first line of the file.
-                Create a trimlog for every data set writing "-trimlog" without a path, it will be saved in
-                the same folder as the single or "_1" input file.
--tt INT         Trimmomatic threads. Specify either within -to or with -tt. [1]
--trim STR       A file containing Trimmomatic trimmer in the first line in the particular order they should be
-                executed.
-                If trimming overrepresented k-mers, the "ILLUMINACLIP" will be inserted after the last
-                specified "ILLUMINACLIP".
--k INT          K-mer length to screen for overrepresentaion with FastQC between 2 and 10. [7].
--nok            No overrepresentation screening of k-mers. Trim each set once and create a FastQC report.
-                Recommended for RNA-seq. [off]
--v              Verbose. Print executed commands of Trimmomatic, FastQC and MultiQC to STDOUT and log file.
-                [off]
--tp STR         Trimmomatic path. The whole path to the Trimmomatic jar file. Specify if "trimmomatic" is not
-                in your $PATH.
--fqcp STR       FastQC path. The whole path to the FastQC executable. Specify if "fastqc" is not in your
-                $PATH.
--mqcp STR       MultiQC path. The whole path to the MultiQC executable. Specify if "multiqc" is not in your
-                $PATH and you want to automatically execute MultiQC.
--rn             Rename files according the folder they are placed in. [off]
--version        Print version number and exit.
--h or -help     Print this help and exit.
+Options: [default]
+	-d STR		Root directory for automatic input of multiple data sets. The file containing
+			overrepresented k-mers (kmer.fa) and the autotrim log file (autotrim.log) will be
+			saved in this directory.
+	-fofn STR	File of file names containing tab-seperated paths to one data set per line.
+	-log STR	Specify the path to save the file containing overrepresented k-mers (kmer.fa) and
+			the log file of autotrim (autotrim.log) if using -fofn.
+	-to STR		A file containing Trimmomatic options that should be used. All options need to be
+			in the first line of the file.
+			Create a trimlog for every data set writing "-trimlog" without a path, it will be
+			saved in the same folder as the single or "_1" input file.
+	-tt INT		Trimmomatic threads. Specify either within -to or with -tt. [1]
+	-trim STR	A file containing Trimmomatic trimmer in the first line in the particular order
+			they should be executed.
+			If trimming overrepresented k-mers, the "ILLUMINACLIP" will be inserted after the
+			last specified "ILLUMINACLIP".
+	-k INT		K-mer length to screen for overrepresentaion with FastQC between 2 and 10. [7].
+	-nok		No overrepresentation screening of k-mers. Trim each set once and create a FastQC
+			report.
+			Recommended for RNA-seq. [off]
+	-v		Verbose. Print executed commands of Trimmomatic, FastQC and MultiQC to STDOUT and
+			log file. [off]
+	-tp STR		Trimmomatic path. The whole path to the Trimmomatic jar file. Specify if
+			"trimmomatic" is not in your $PATH.
+	-fqcp STR	FastQC path. The whole path to the FastQC executable. Specify if "fastqc" is not
+			in your $PATH.
+	-mqcp STR	MultiQC path. The whole path to the MultiQC executable. Specify if "multiqc" is
+			not in your $PATH and you want MultiQC automatically executed.
+	-rn		Rename files according the folder they are placed in. [off]
+	-version	Print version number and exit.
+	-h or -help	Print this help and exit.
 ```
 
 ## Citation
@@ -89,6 +83,9 @@ If you use this tool please cite:
 
 Additional to the dependencies:
 
-- Bolger AM, Lohse M, Usadel B (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15):2114–2120. [https://doi.org/10.1093/bioinformatics/btu170](https://doi.org/10.1093/bioinformatics/btu170)
-- Andrews S (2010). FastQC: a quality control tool for high throughput sequence data. [http://www.bioinformatics.babraham.ac.uk/projects/fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
-- Ewels P, Magnusson M, Lundin S, Käller M (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. *Bioinformatics*, 32(19):3047–3048. [https://doi.org/10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354)
+- Trimmomatic  
+Bolger AM, Lohse M, Usadel B (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15):2114–2120. [https://doi.org/10.1093/bioinformatics/btu170](https://doi.org/10.1093/bioinformatics/btu170)
+- FastQC  
+Andrews S (2010). FastQC: a quality control tool for high throughput sequence data. [http://www.bioinformatics.babraham.ac.uk/projects/fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
+- MultiQC  
+Ewels P, Magnusson M, Lundin S, Käller M (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. *Bioinformatics*, 32(19):3047–3048. [https://doi.org/10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354)