Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine). It also supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts), SIMDe and dispatching.
To build spoa run the following commands:
git clone --recursive https://github.com/rvaser/spoa.git spoa
cd spoa && mkdir build && cd build
cmake -Dspoa_build_executable=ON -DCMAKE_BUILD_TYPE=Release .. && make
./bin/spoa
which will display the following usage:
usage: spoa [options ...] <sequences>
# default output is stdout
<sequences>
input file in FASTA/FASTQ format (can be compressed with gzip)
options:
-m <int>
default: 5
score for matching bases
-n <int>
default: -4
score for mismatching bases
-g <int>
default: -8
gap opening penalty (must be non-positive)
-e <int>
default: -6
gap extension penalty (must be non-positive)
-q <int>
default: -10
gap opening penalty of the second affine function
(must be non-positive)
-c <int>
default: -4
gap extension penalty of the second affine function
(must be non-positive)
-l, --algorithm <int>
default: 0
alignment mode:
0 - local (Smith-Waterman)
1 - global (Needleman-Wunsch)
2 - semi-global
-r, --result <int>
default: 0
result mode:
0 - consensus (FASTA)
1 - multiple sequence alignment (FASTA)
2 - 0 & 1 (FASTA)
3 - partial order graph (GFA)
4 - 0 & 3 (GFA)
-d, --dot <file>
output file for the partial order graph in DOT format
-s, --strand-ambiguous
for each sequence pick the strand with the better alignment
--version
prints the version number
-h, --help
prints the usage
gap mode:
linear if g >= e
affine if g <= q or e >= c
convex otherwise (default)
Various options can be enabled while running cmake:
spoa_optimize_for_native
: builds with-march=native
spoa_optimize_for_portability
: builds with-msse4.1
spoa_use_simde
: builds with SIMDe for porting vectorized codespoa_use_simde_nonvec
: uses SIMDe library for nonvectorized codespoa_use_simde_openmp
: uses SIMDe support for OpenMP SIMDspoa_generate_dispatch
: uses SIMDe to generate x86 dispatch
If you would like to add spoa as a library to your project via CMake, add the following:
if (NOT TARGET spoa)
add_subdirectory(<path_to_submodules>/spoa EXCLUDE_FROM_ALL)
endif ()
target_link_libraries(<your exe> spoa)
- gcc 4.8+ or clang 3.5+
- cmake 3.9+
- zlib (executable only)
#include <iostream>
#include "spoa/spoa.hpp"
int main(int argc, char** argv) {
std::vector<std::string> sequences = {
"CATAAAAGAACGTAGGTCGCCCGTCCGTAACCTGTCGGATCACCGGAAAGGACCCGTAAAGTGATAATGAT",
"ATAAAGGCAGTCGCTCTGTAAGCTGTCGATTCACCGGAAAGATGGCGTTACCACGTAAAGTGATAATGATTAT",
"ATCAAAGAACGTGTAGCCTGTCCGTAATCTAGCGCATTTCACACGAGACCCGCGTAATGGG",
"CGTAAATAGGTAATGATTATCATTACATATCACAACTAGGGCCGTATTAATCATGATATCATCA",
"GTCGCTAGAGGCATCGTGAGTCGCTTCCGTACCGCAAGGATGACGAGTCACTTAAAGTGATAAT",
"CCGTAACCTTCATCGGATCACCGGAAAGGACCCGTAAATAGACCTGATTATCATCTACAT"
};
auto alignment_engine = spoa::AlignmentEngine::Create(
spoa::AlignmentType::kNW, 3, -5, -3); // linear gaps
spoa::Graph graph{};
for (const auto& it : sequences) {
auto alignment = alignment_engine->Align(it, graph);
graph.AddAlignment(alignment, it);
}
auto consensus = graph.GenerateConsensus();
std::cerr << ">Consensus LN:i:" << consensus.size() << std::endl
<< consensus << std::endl;
auto msa = graph.GenerateMultipleSequenceAlignment();
for (const auto& it : msa) {
std::cerr << it << std::endl;
}
return 0;
}
To build and run spoa unit tests run the following commands:
git clone --recursive https://github.com/rvaser/spoa.git spoa
cd spoa && mkdir build && cd build
cmake -Dspoa_build_tests=ON -DCMAKE_BUILD_TYPE=Release .. && make
./bin/spoa_test
- gtest
This work has been supported in part by Croatian Science Foundation under projects UIP-11-2013-7353 and IP-2018-01-5886.