Raven

Raven is a de novo genome assembler for long uncorrected reads.

Usage

To build raven run the following commands (< 30s):

git clone https://github.com/lbcb-sci/raven && cd raven && mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release .. && make

which will create raven executable and unit tests (running make install will install the executable to your system). Running the executable will display the following usage:

usage: raven [options ...] <sequences> [<sequences> ...]

  # default output is to stdout in FASTA format
  <sequences>
    input file in FASTA/FASTQ format (can be compressed with gzip)

  options:
    -k, --kmer-len <int>
      default: 15
      length of minimizers used to find overlaps
    -w, --window-len <int>
      default: 5
      length of sliding window from which minimizers are sampled
    -f, --frequency <double>
      default: 0.001
      threshold for ignoring most frequent minimizers
    -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 assembly graph in GFA format
    --resume
      resume previous run from last checkpoint
    --disable-checkpoints
      disable checkpoint file creation
    -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 <int>
      default: 0
      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 <int>
      default: 0
      number of batches for CUDA accelerated alignment

Build options

• raven_build_tests: build unit tests
• racon_enable_cuda: build with NVIDIA CUDA support

Dependencies

• gcc 4.8+ | clang 4.0+
• cmake 3.11+
• zlib 1.2.8+

Hidden

• lbcb-sci/racon/tree/library 3.0.2
• rvaser/bioparser 3.0.13
• (raven_test) google/googletest 1.10.0

Other options

Brew

Install Linuxbrew and run the following command:

brew install brewsci/bio/raven-assember

Conda

Install conda and run the following command:

conda install -c bioconda raven-assembler

Acknowledgment

This work has been supported in part by the Genome Institute of Singapore (A*STAR), by the Croatian Science Foundation under 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 grant KK.01.1.1.01.0009 (DATACROSS).