Ram is a c++ implementation of minimap with few modifications.
To build ram run the following commands:
git clone --recursive https://github.com/dbabojelic/ram.git ram
cd ram && mkdir build && cd build
cmake -Dram_build_executable=ON -DCMAKE_BUILD_TYPE=Release .. && make
./bin/ramwhich 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 will be applied sequentially as specified, example:
$ ram -w10 -k19 -w5 reads.fastq
will result in w = 5
options:
-k, --kmer-length <int>
default: 15
length of minimizers
-w, --window-length <int>
default: 5
length of sliding window from which minimizers are found
-H, --hpc
Use homopolymer-compressed (HPC) minimizers
-r, --robust-winnowing
Use robust winnowing while extracting minimizers (idea taken from Winnowmap)
-f, --frequency-threshold <float>
default: 0.001
threshold for ignoring most frequent minimizers
-M, --Micromize
use only a portion of all minimizers
-p, --Micromize-factor <float>
Expect to get a floating number between 0 and 1
When using micromizers reduce the number of minimizers to <float> smallest ones
If zero: number of taken micromizers will be bounded by the value of sequence_len / k
default: 0
-N, --Micromize-extend <int>
when using micromizers always take first and last <int> minimizers
default: 0
-K, --begin-end <int>
when greater than zero, begin-end strategy will be used
default: 0
-m <int>
default: 100
discard chains with chaining score less than <int>
-g <int>
default: 10000
stop chain elongation if there are no minimizer withing <int>-BP
-n <int>
default: 4
discard chains consisting of less then <int> minimizers
-b --best-n <int>
default: 0
choose only <int> best hits; if zero all hits will be chosen
-i, --reduce-win-sz <int>
default: 0
if zero does nothing; otherwise one more hierarchical level of minimizing procedure is applied (with given window size)
-x, --preset-options ava|map
default: none
preset options; applies multiple options at the same time;
this options will be overwritten if used with other options;
available preset options strings:
ava: all-vs-all alignment (-k19 -w5 -m100 -g10000 -n4)
map: read to reference mapping (-k19 -w10 -m40 -g5000 -n3 -b5)
-t, --threads <int>
default: 1
number of threads
--version
prints the version number
-h, --help
prints the usageIf you would like to add ram as a library to your project via CMake, add the following:
if (NOT TARGET ram)
add_subdirectory(<path_to_submodules>/ram EXCLUDE_FROM_ALL)
endif ()
target_link_libraries(<your_exe> ram)- gcc 4.8+ or clang 3.5+
- cmake 3.9+
- zlib (for binary only)
To build ram unit tests run the following commands:
git clone https://github.com/dbabojelic/ram.git ram
cd ram && mkdir build && cd build
cmake -Dram_build_tests=ON -DCMAKE_BUILD_TYPE=Release .. && make
./bin/ram_test- gtest
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).