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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, ...).
Clone the repository, or download the source. Make sure that your system supplies the following dependencies for FastqPuri.
cmake
(at least version 2.8),C
compiler supporting the c11
standard (change the compiler flags otherwise),PANDOC.md
),Rscript
(optional),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.
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.
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
).trimFilterDS
: performs the filtering process for double stranded data (see README_trimFilterDS.md
).An exemplar work flow could be:
Qreport
Sreport
makeBloom
trimFilter
or trimFilterDS
Qreport
Sreport
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
Paula Pérez Rubio
GPL v3 (see LICENSE.txt)