Ram

Ram is a c++ implementation of minimap with few modifications.

Usage

To build ram run the following commands:

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

which will create ram library, executable and unit tests. Running the executable will display the following usage:

usage: ram [options ...] <target> [<sequences>]

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

  options:
    -k, --kmer-length <int>
      default: 15
      length of minimizers
    -w, --window-length <int>
      default: 5
      length of sliding window from which minimizers are sampled
    -f, --frequency-threshold <float>
      default: 0.001
      threshold for ignoring most frequent minimizers
    --bandwidth <int>
      default: 500
      size of bandwidth in which minimizer hits can be chained
    --chain <int>
      default: 4
      minimal number of chained minimizer hits in overlap
    --matches <int>
      default: 100
      minimal number of matching bases in overlap
    --gap <int>
      default: 10000
      maximal gap between minimizer hits in a chain
    --minhash
      use only a portion of all minimizers
    -t, --threads <int>
      default: 1
      number of threads
    --version
      prints the version number
    -h, --help
      prints the usage

Running make install will install the executable. In order to install the library, both biosoup and thread_pool (see Dependencies) need to be installed beforehand, and option ram_install used while configuring the build. Once the library is installed, a package will be copied to your system that can be searched and linked with:

find_package(ram)
target_link_libraries(<target> ram::ram)

On the other hand, you can include ram as a submodule and add it to your project with the following:

if (NOT TARGET ram)
  add_subdirectory(<path_to_submodules>/ram EXCLUDE_FROM_ALL)
endif ()
target_link_libraries(<target> ram::ram)

Build options

ram_install: generate library install target
ram_build_exe: build executable
ram_build_tests: build unit tests

Dependencies

gcc 4.8+ | clang 3.5+
cmake 3.11+
pthread
(ram_exe)(ram_test) zlib 1.2.8+

Hidden

rvaser/biosoup 0.10.0
rvaser/thread_pool 4.0.0
(ram_exe)(ram_test) rvaser/bioparser 3.0.13
(ram_test) google/googletest 1.10.0

Acknowledgement

This work has been supported in part by the European Regional Development Fund under the grant KK.01.1.1.01.0009 (DATACROSS) and in part by the Croatian Science Foundation under the project Single genome and metagenome assembly (IP-2018-01-5886).