diff --git a/cudapoa/src/cudapoa_kernels.cu b/cudapoa/src/cudapoa_kernels.cu
diff --git a/cudapoa/src/cudapoa_kernels.cuh b/cudapoa/src/cudapoa_kernels.cuh
diff --git a/cudapoa/src/cudapoa_nw.cu b/cudapoa/src/cudapoa_nw.cu
diff --git a/cudapoa/src/cudapoa_nw_banded.cu b/cudapoa/src/cudapoa_nw_banded.cu
diff --git a/cudapoa/src/cudapoa_topsort.cu b/cudapoa/src/cudapoa_topsort.cu
diff --git a/cudapoa/tests/CMakeLists.txt b/cudapoa/tests/CMakeLists.txt
diff --git a/cudapoa/tests/Test_CudapoaAddAlignment.cpp b/cudapoa/tests/Test_CudapoaAddAlignment.cpp
diff --git a/cudapoa/tests/Test_CudapoaBatch.cpp b/cudapoa/tests/Test_CudapoaBatch.cpp
diff --git a/cudapoa/tests/Test_CudapoaBatchEnd2End.cpp b/cudapoa/tests/Test_CudapoaBatchEnd2End.cpp
diff --git a/cudapoa/tests/Test_CudapoaGenerateConsensus.cpp b/cudapoa/tests/Test_CudapoaGenerateConsensus.cpp
diff --git a/cudapoa/tests/Test_CudapoaGenerateMSA2.cpp b/cudapoa/tests/Test_CudapoaGenerateMSA2.cpp
diff --git a/cudapoa/tests/Test_CudapoaNW.cpp b/cudapoa/tests/Test_CudapoaNW.cpp
diff --git a/cudapoa/tests/Test_CudapoaTopSort.cpp b/cudapoa/tests/Test_CudapoaTopSort.cpp
diff --git a/cudapoa/tests/basic_graph.hpp b/cudapoa/tests/basic_graph.hpp
diff --git a/cudapoa/tests/sorted_graph.hpp b/cudapoa/tests/sorted_graph.hpp
diff --git a/docs/README-SDK.md b/docs/README-SDK.md
diff --git a/docs/todo.txt b/docs/todo.txt
diff --git a/pyclaragenomics/README.md b/pyclaragenomics/README.md
diff --git a/pyclaragenomics/bin/assembly_evaluator b/pyclaragenomics/bin/assembly_evaluator
diff --git a/pyclaragenomics/bin/genome_simulator b/pyclaragenomics/bin/genome_simulator
diff --git a/pyclaragenomics/claragenomics/__init__.py b/pyclaragenomics/claragenomics/__init__.py
diff --git a/pyclaragenomics/claragenomics/bindings/__init__.py b/pyclaragenomics/claragenomics/bindings/__init__.py
diff --git a/pyclaragenomics/claragenomics/bindings/cuda.pyx b/pyclaragenomics/claragenomics/bindings/cuda.pyx
diff --git a/pyclaragenomics/claragenomics/bindings/cuda_runtime_api.pxd b/pyclaragenomics/claragenomics/bindings/cuda_runtime_api.pxd
diff --git a/pyclaragenomics/claragenomics/bindings/cudapoa.pxd b/pyclaragenomics/claragenomics/bindings/cudapoa.pxd
diff --git a/pyclaragenomics/claragenomics/bindings/cudapoa.pyx b/pyclaragenomics/claragenomics/bindings/cudapoa.pyx
diff --git a/pyclaragenomics/claragenomics/io/__init__.py b/pyclaragenomics/claragenomics/io/__init__.py
diff --git a/pyclaragenomics/claragenomics/io/fastaio.py b/pyclaragenomics/claragenomics/io/fastaio.py
diff --git a/pyclaragenomics/claragenomics/io/utils.py b/pyclaragenomics/claragenomics/io/utils.py
diff --git a/pyclaragenomics/claragenomics/simulators/__init__.py b/pyclaragenomics/claragenomics/simulators/__init__.py
diff --git a/pyclaragenomics/claragenomics/simulators/genomesim.py b/pyclaragenomics/claragenomics/simulators/genomesim.py
diff --git a/pyclaragenomics/claragenomics/simulators/readsim.py b/pyclaragenomics/claragenomics/simulators/readsim.py
diff --git a/pyclaragenomics/claragenomics/test/__init__.py b/pyclaragenomics/claragenomics/test/__init__.py
diff --git a/pyclaragenomics/claragenomics/utilities/__init__.py b/pyclaragenomics/claragenomics/utilities/__init__.py
diff --git a/pyclaragenomics/claragenomics/utilities/utilities.py b/pyclaragenomics/claragenomics/utilities/utilities.py
diff --git a/pyclaragenomics/claragenomics/wrappers/__init__.py b/pyclaragenomics/claragenomics/wrappers/__init__.py
diff --git a/pyclaragenomics/claragenomics/wrappers/wrappers.py b/pyclaragenomics/claragenomics/wrappers/wrappers.py
diff --git a/pyclaragenomics/requirements.txt b/pyclaragenomics/requirements.txt
diff --git a/pyclaragenomics/samples/sample_cudapoa b/pyclaragenomics/samples/sample_cudapoa
diff --git a/pyclaragenomics/setup.cfg b/pyclaragenomics/setup.cfg
diff --git a/pyclaragenomics/setup.py b/pyclaragenomics/setup.py
diff --git a/...cs/claragenomics/test/data/assembly_GT.fa → pyclaragenomics/test/data/assembly_GT.fa b/...cs/claragenomics/test/data/assembly_GT.fa → pyclaragenomics/test/data/assembly_GT.fa
diff --git a/...s/claragenomics/test/data/assembly_GT.gfa → pyclaragenomics/test/data/assembly_GT.gfa b/...s/claragenomics/test/data/assembly_GT.gfa → pyclaragenomics/test/data/assembly_GT.gfa
diff --git a/...s/claragenomics/test/data/overlaps_GT.paf → pyclaragenomics/test/data/overlaps_GT.paf b/...s/claragenomics/test/data/overlaps_GT.paf → pyclaragenomics/test/data/overlaps_GT.paf
diff --git a/...ics/test/data/overlaps_on_assembly_GT.paf → ...ics/test/data/overlaps_on_assembly_GT.paf b/...ics/test/data/overlaps_on_assembly_GT.paf → ...ics/test/data/overlaps_on_assembly_GT.paf
diff --git a/...data/polished_assembly_CPU_subgraph_GT.fa → ...data/polished_assembly_CPU_subgraph_GT.fa b/...data/polished_assembly_CPU_subgraph_GT.fa → ...data/polished_assembly_CPU_subgraph_GT.fa
diff --git a/...omics/claragenomics/test/data/reads.fasta → pyclaragenomics/test/data/reads.fasta b/...omics/claragenomics/test/data/reads.fasta → pyclaragenomics/test/data/reads.fasta
diff --git a/...enomics/claragenomics/test/data/ref.fasta → pyclaragenomics/test/data/ref.fasta b/...enomics/claragenomics/test/data/ref.fasta → pyclaragenomics/test/data/ref.fasta
diff --git a/pyclaragenomics/test/test_cuda_bindings.py b/pyclaragenomics/test/test_cuda_bindings.py
diff --git a/pyclaragenomics/test/test_cudapoa_bindings.py b/pyclaragenomics/test/test_cudapoa_bindings.py
diff --git a/...aragenomics/test/test_genome_simulator.py → ...aragenomics/test/test_genome_simulator.py b/...aragenomics/test/test_genome_simulator.py → ...aragenomics/test/test_genome_simulator.py
diff --git a/...laragenomics/test/test_read_simulators.py → pyclaragenomics/test/test_read_simulators.py b/...laragenomics/test/test_read_simulators.py → pyclaragenomics/test/test_read_simulators.py
diff --git a/...omics/claragenomics/test/test_wrappers.py → pyclaragenomics/test/test_wrappers.py b/...omics/claragenomics/test/test_wrappers.py → pyclaragenomics/test/test_wrappers.py