pythseq / fastqpuri

fastq quality assessment and filtering tool

FastqPuri, an fq quality control and filter tool

Software and source code of FastqPuri. It creates quality reports of fastq files and filters them removing low quality reads, reads containing too many N's or contamination reads (unwanted rRNA reads, impurities coming from another organism, ...).

Installation

Clone the repository, or download the source. Make sure that your system supplies the following dependencies for FastqPuri.

• OS: Linux (clang, gcc), Mac OS (clang, gcc), OpenBSD (clang)
• cmake (at least version 2.8),
• a C compiler supporting the c11 standard (change the compiler flags otherwise),
• pandoc (optional, see documentation in PANDOC.md),
• Rscript (optional),
• Following R packages installed (optional):
  • pheatmap
  • knitr
  • rmarkdown

NOTE: FastqPuri will work without the optional dependencies but will skip creating html reports if they are not available.

$ cmake -H. -Bbuild/ [-DRSCRIPT=/path/to/my/R/bin/Rscript ... ]
$ cd build 
$ make 

When running cmake, there are some variables you can set using the option -D followed by the variable name. This variables are,

• CMAKE_C_COMPILER: C compiler (default gcc)
• CMAKE_C_FLAGS: compiler flags (default -Wall -O3 -march=native -std=c11).
• PANDOC: pandoc executable (default pandoc),
• RSCRIPT: Rscript executable (default Rscript),
• READ_MAXLEN: Maximum Illumina read length (default 400),
• RMD_QUALITY_REPORT: path to quality_report.Rmd,
• RMD_SUMMARY_REPORT: path to summary_report.Rmd,

The executables will be created in the folder bin.

WARNING: do not move the executables that depend on R scripts, anywhere else, unless you also move the corresponding R scripts respecting the local folder structure.

Executables

• Qreport: creates a quality report in html format (see README_Qreport.md),
• Sreport: creates a summary report in html format on a set of samples, regarding either the original files or the filtering process (see README_Sreport.md),
• makeBloom: creates a bloom filter from a fata file of a certain size, and stores it in a file (see README_makeBloom.md)
• makeTree: creates a tree of a certain depth from a fasta file and stores it in a file (see README_makeTree.md),
• trimFilter: performs the filtering process for single-end data (see README_trimFilter.md).
• trimFilterPE: performs the filtering process for double stranded data (see README_trimFilterPE.md).

An exemplar work flow could be:

• Qreport
• Sreport
• makeBloom
• trimFilter or trimFilterPE
• Qreport
• Sreport

Documentation of the code

A Doxygen documentation of the code is available:

• html version under the folder html (open index.html with a browser).
• pdf version: latex/refman.pdf

Contributors

Paula Pérez Rubio

License

GPL v3 (see LICENSE.txt)