├── .gitignore ├── .gitmodules ├── Makefile ├── README.md ├── asmtools ├── add_edges.py ├── assemble_gml.py ├── bridge_removal.py ├── bubble_identification.py ├── color.py ├── compare_numbers.py ├── create_gml.py ├── elba.overlap.paf ├── elba.string.paf ├── find_bubbles.py ├── reads.fa ├── ref.fa ├── remove_tips.py └── star_resolution.py ├── assembly_graph.py ├── example_medium ├── reads.fa ├── reads.fa.fai └── ref.fa ├── include ├── Bloom.hpp ├── CC.hpp ├── ContigGeneration.hpp ├── DistributedFastaData.hpp ├── DistributedPairwiseRunner.hpp ├── DnaBuffer.hpp ├── DnaSeq.hpp ├── ELBALogger.hpp ├── FastaIndex.hpp ├── HashFuncs.hpp ├── HyperLogLog.hpp ├── Kmer.hpp ├── KmerOps.hpp ├── Logger.hpp ├── MPITimer.hpp ├── Overlap.hpp ├── PairwiseAlignment.hpp ├── PruneChimeras.hpp ├── ReadOverlap.hpp ├── SharedSeeds.hpp ├── TransitiveReduction.hpp ├── XDropAligner.hpp ├── common.h └── compiletime.h ├── install.sh ├── licenses ├── hipmer.txt ├── license.txt └── pastis.txt ├── paf2gml.py ├── reads.fa ├── reads.fa.fai ├── ref.fa ├── runs └── simfor.py ├── runtests.sh ├── script ├── analysis.sh ├── corigpu-job-ecoli.sh ├── elba_bounds.py ├── extract_times.py ├── hydra-script.py ├── igraph-elba.r ├── job.haswell.clr-human-10x.128n ├── job.haswell.hifi-celegans.40x.128n ├── job.haswell.hifi-celegans.40x.18n ├── job.haswell.hifi-celegans.40x.32n ├── job.haswell.hifi-celegans.40x.50n ├── job.haswell.hifi-celegans.40x.72n ├── job.haswell.rice30x.128n ├── job.haswell.rice30x.50n ├── job.haswell.rice30x.72n ├── job.haswell.yeast.383x.18n ├── job.haswell.yeast.383x.32n ├── job.haswell.yeast.383x.50n └── job.haswell.yeast.383x.72n ├── src ├── Bloom.cpp ├── ContigGeneration.cpp ├── DistributedFastaData.cpp ├── DistributedPairwiseRunner.cpp ├── DnaBuffer.cpp ├── DnaSeq.cpp ├── ELBALogger.cpp ├── FastaIndex.cpp ├── HashFuncs.cpp ├── HyperLogLog.cpp ├── Kmer.cpp ├── KmerOps.cpp ├── Logger.cpp ├── Overlap.cpp ├── PairwiseAlignment.cpp ├── PruneChimeras.cpp ├── ReadOverlap.cpp ├── SharedSeeds.cpp ├── TransitiveReduction.cpp ├── XDropAligner.cpp ├── libbloom │ ├── CMakeLists.txt │ ├── LICENSE │ ├── Makefile │ ├── README │ ├── bloom.c │ ├── bloom.h │ ├── bloom64.c │ ├── bloom64.h │ ├── murmur2 │ │ ├── CMakeLists.txt │ │ ├── MurmurHash2.c │ │ ├── README │ │ └── murmurhash2.h │ └── test.c └── main.cpp ├── test.py └── usage.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/ELBA/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/ELBA/HEAD/.gitmodules -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/ELBA/HEAD/Makefile 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