denovo-qassembler

denovo-qassembler is a software package designed to reconstruct quaispecies variants from a set of next-generation sequencing reads without using a reference sequence.

• Recent Changes
• Building
  • Dependencies
  • Running cmake
  • Disabling log4cxx
• Running
  • Examples
• Contact

Download

You can download the source code for the current release of denovo-qassembler below:

denovo qassembler 1.0.3

Older Versions

denovo qassembler 1.0.1

denovo qassembler 1.0.2

Recent Changes

1.0.3

• Fixed abundance estimation bug: edge weights were not reset prior to estimating abundance.
• Don't use log1p from boost to calculate relative abundance, use log from cmath.

1.0.2

• Fixed edge weight bug: edge weights are stored in an unsigned container, when decreasing edge weights make sure to check that the amount to decrease by is less than the current edge weight.
• Sort starting point vertices before constructing paths so that reconstructed paths are reproducible between executions.

Building

Dependencies

denovo-qassembler uses cmake as a dependency detection and build automation tool. Binaries for cmake are available for most operating systems. denovo-qassembler uses the Boost C++ Libraries extensively for graph construction as well as pointer management. Finally, denovo-qassembler can optionally use log4cxx to display logging information with high granularity.

To install all dependencies in Ubuntu, you can use apt-get:

sudo apt-get install g++ build-essential cmake libboost-all-dev liblog4cxx10-dev

To install all dependencies in Fedora, you can use yum:

sudo yum install gcc-c++ cmake boost-devel log4cxx-devel zlib-devel

To install all dependencies in CentOS or Scientific Linux, you can use yum:

sudo yum install gcc-c++ cmake boost-devel zlib-devel # CentOS and Scientific Linux do not ship log4cxx

Running cmake

One of the primary features of cmake is out-of-source builds, meaning that all binary files will be built outside of the source directory. Out-of-source builds make for a cleaner development environment because binary files are not scattered throughout your source directory.

To build denovo-qassembler, extract the source tarball, change into the build directory, run cmake, then make:

tar xf denovo-qassembler-1.0.3.tar.gz
cd denovo-qassembler-1.0.3/build
cmake ..
make

denovo-qassembler has a comprehensive test suite which can be executed prior to installation to ensure correctness of the build. To test denovo-qassembler, run:

make test

denovo-qassembler can be installed to the default system directories (i.e., /usr/local/bin and /usr/local/lib) by running:

sudo make install

Disabling log4cxx

If log4cxx does not ship with your operating system (or you wish to disable it), you can still get some logging information from denovo-qassembler by specifying log severity levels at compile time.

To disable log4cxx, pass cmake a compile time:

cmake -DUSE_LOG4CXX=off ..

If you would like to enable some level of logging, you can run:

cmake -DUSE_LOG4CXX=off -DLOGGING_SEVERITY=i

where 0 <= i <= 2 and larger values for i result in more log output. All logging written by denovo-qassembler when log4cxx is disabled is written to stderr.

Running

denovo-qassembler has a variety of input options which change the way that variants are reconstructed and the way that relative abundance is calculated.

Option	Description	Default	Type	Required?
--help	Prints out all options and their description.	disabled	Boolean	No
--input-sequences f	fasta/fastq file containing sequencing reads.	N/A	String	Yes
	Files compressed with gzip are allowed.
--kmer-size i	The k-mer size used to construct the de Bruijn graph (k must be odd)	31	Integer	No
--pre-hash	Hash all reads prior to constructing the graph.	disabled	Boolean	No
	May improve graph construction performance when used with --aggressive-edge-removal.
--aggressive-edge-removal i	Remove edges from constructed graphs whose edge weight is below i.	N/A	Integer	No
--print-graphs	Print the graph structures in DOT format, suitable for rendering with graphviz.	disabled	Boolean	No
--graph-dir d	Write DOT formatted graph files to the specified directory d.	graphs/	String	No
	Directory is created if necessary.
--minimum-bases i	Remove disconnected sub-graphs with a single vertex referring to fewer	N/A	Integer	No
	than i significant base pairs.
--sequences	Print the sequences corresponding to the paths generated by the path construction algorithm.	N/A	Boolean	No
--sequence-dir d	Write sequences to the specified directory d. Directory is created if necessary.	sequences/	String	No
--path-method m	Specify the method for constructing paths through the de Bruijn graph, one of	proportional	String	No
	proportional, markov, or random.
--epsilon e	Specify maximum allowable difference e between proportionally similar edge weights.	0.01	Double	No
--minimum-length i	Do not report sequences that have a length less than i.	N/A	Integer	No
--abundance-method m	Specify the method for estimating relative abundance,	markov-chain	String	No
	one of markov-chain or forward-algorithm.
--log-config f	Specify a custom log4cxx configuration file.	N/A	String	No

Examples

Given a compressed fasta file containing reads called reads.fna.gz, you could print out the set of de Bruijn graphs constructed using a k-mer size of 127:

denovo-qassembler --input-sequences reads.fna.gz --kmer-size 127 --print-graphs --graphs-dir read-graphs

Another example is to reconstruct a set of variants using the Proportional method, estimate relative abundance with the markov-chain method and remove edges with edge weight below 2:

denovo-qassembler --input-sequences reads.fna.gz --kmer-size 127 --aggressive-edge-removal 2 --sequences --sequence-dir read-sequences --abundance-method markov-chain

Contact

For more information about denovo-qassembler, please contact:

• Franklin Bristow: [email protected]
• Gary Van Domselaar: [email protected]
• Michael Domaratzki: [email protected]