Waldvogel A-M, Schell T
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 $PATH and -mqcp is not specified.
Autotrim distinguishes automatically between paired and single end data.
- Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic
- FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Optional
- MultiQC: http://multiqc.info/
- From FastQC version 0.11.6 the k-mer plot is disabled by default but is needed in Autotrim. To enable it, edit
FastQC/Configuration/limits.txtby changing the1in the end of the line starting withkmerto0.
Optional
- If you don't want to specify
-tp,trimmomaticshould be in your$PATH. To do so, create an executable file namedtrimmomaticwith the contentjava -jar /path/to/trimmomatic.jar $*in a directory that is your$PATH. Be sure to write the actual path to thejarfile.
There are two different ways to specify the input files:
- Multiple folders containing one or two fastq files are in the same directory. The fastq file(s) need to end with
.f(ast)q(.gz). For paired data the two fastq files have to end with_1.f(ast)q(.gz)and_2.f(ast)q(.gz). Folders containing more than two fastq files or paired data without matching the criteria are skipped. - File of file names containing a path to a single end fastq or two tab seperated paths for paired end data per line. The files for paired end data don't have to be in the same folder nor any special file names.
While choosing a root direcory will skip the subdirectory when it contains more than two fastq files (e.g. output), the file of file names option will overwirte existing files without asking!
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 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.
If you use this tool please cite:
- Waldvogel A-M, Wieser A, Schell T, Patel S, Schmidt H et al. (2018). The genomic footprint of climate adaptation in Chironomus riparius. Molecular Ecology, 27(6):1439–1456. https://doi.org/10.1111/mec.14543
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
- Andrews S (2010). FastQC: a quality control tool for high throughput sequence data. 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