Tool for de novo genome assembly of long uncorrected reads.
Raven is an assembler for raw reads generated by third generation sequencing. It first finds overlaps between reads by chaining minimizer hits (submodule Ram which is minimap turned into a library), creates an assembly graph and simplifies it (code from Rala), and polishes the obtained contigs with partial order alignment (submodule Racon).
Raven takes as input a single file containing raw reads in FASTA/FASTQ format (can be compressed with gzip) and outputs a set of contigs with high accuracy in FASTA format to stdout.
- gcc 4.8+ or clang 3.4+
- cmake 3.2+
- gcc 5.0+
- cmake 3.10+
- CUDA 9.0+
To install Raven run the following commands:
git clone --recursive https://github.com/lbcb-sci/raven.git raven cd raven mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release .. make
After successful installation, an executable named
raven will appear in
Optionally, you can run
sudo make install to install raven executable to your machine.
Note: if you omitted
git clone, run
git submodule update --init --recursive before proceeding with compilation.
racon makes use of NVIDIA's ClaraGenomicsAnalysis SDK for CUDA accelerated polishing and alignment.
To build with CUDA support, add
-Dracon_enable_cuda=ON while running
cmake. If CUDA support is unavailable, the
cmake step will report an error.
Note that the CUDA support flag does not produce a new binary target. Instead it augments the existing
raven binary itself.
cd build cmake -DCMAKE_BUILD_TYPE=Release -Dracon_enable_cuda=ON .. make
Install Linuxbrew and run the following command:
brew install brewsci/bio/raven-assember
Install conda and run the following command:
conda install -c bioconda raven-assembler
raven is as following:
raven [options ...] <sequences> <sequences> input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences options: -p, --polishing-rounds <int> default: 2 number of times racon is invoked -m, --match <int> default: 3 score for matching bases -n, --mismatch <int> default: -5 score for mismatching bases -g, --gap <int> default: -4 gap penalty (must be negative) --graphical-fragment-assembly <string> prints the assemblg graph in GFA format -t, --threads <int> default: 1 number of threads --version\ prints the version number -h, --help prints the usage (only available when built with CUDA) -c, --cuda-poa-batches default: 1 number of batches for CUDA accelerated polishing -b, --cuda-banded-alignment use banding approximation for polishing on GPU (only applicable when -c is used) -a, --cuda-alignment-batches number of batches for CUDA accelerated alignment
This work has been supported in part by the Croatian Science Foundation under the projects Algorithms for genome sequence analysis (UIP-11-2013-7353) and Single genome and metagenome assembly (IP-2018-01-5886), and in part by the European Regional Development Fund under the grant KK.01.1.1.01.0009 (DATACROSS).