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dawnmydawnmy
committed
added VirGenA
1 parent 71b7e36 commit 632b5fd

11 files changed

+891
-1
lines changed

‎.gitignore

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libs/not_used
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libs/PEHaplo
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libs/PredictHaplo
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libs/virgena
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libs/vicuna.zip
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*.bak
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*.old

‎libs/virgena/VirGenA.jar

33 MB
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‎libs/virgena/config.xml

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<config>
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<Data>
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<pathToReads1>Path to FASTQ file with the first mates</pathToReads1>
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<pathToReads2>Path to FASTQ file with the second mates</pathToReads2>
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<InsertionLength>1000</InsertionLength>
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</Data>
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<Reference>Path to the default reference in FASTA format</Reference>
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<OutPath>Output path</OutPath>
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<ThreadNumber>-1</ThreadNumber>
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<BatchSize>1000</BatchSize>
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<ReferenceSelector>
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<Enabled>false</Enabled>
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<UseMajor>false</UseMajor>
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<ReferenceMSA>Path to reference MSA in FASTA format</ReferenceMSA>
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<PathToUsearch>Path to vsearch executable</PathToUsearch>
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<UclustIdentity>0.95</UclustIdentity>
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<MinReadLength>50</MinReadLength>
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<MinContigLength>1000</MinContigLength>
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<Delta>0.05</Delta>
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<MaxNongreedyComponentNumber>5</MaxNongreedyComponentNumber>
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<MapperToMSA>
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<K>7</K>
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<pValue>0.01</pValue>
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<IndelToleranceThreshold>1.5</IndelToleranceThreshold>
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<RandomModelParameters>
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<Order>4</Order>
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<ReadNum>10000</ReadNum>
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<Step>10</Step>
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</RandomModelParameters>
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</MapperToMSA>
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<Graph>
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<MinReadNumber>5</MinReadNumber>
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<VertexWeight>10</VertexWeight>
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<SimilarityThreshold>0.5</SimilarityThreshold>
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<Debug>false</Debug>
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</Graph>
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<Debug>false</Debug>
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</ReferenceSelector>
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<Mapper>
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<K>5</K>
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<pValue>0.01</pValue>
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<IndelToleranceThreshold>1.25</IndelToleranceThreshold>
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<RandomModelParameters>
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<Order>4</Order>
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<ReadNum>1000</ReadNum>
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<Step>10</Step>
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</RandomModelParameters>
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<Aligner>
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<Match>2</Match>
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<Mismatch>-3</Mismatch>
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<GapOpenPenalty>5</GapOpenPenalty>
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<GapExtensionPenalty>2</GapExtensionPenalty>
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</Aligner>
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</Mapper>
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<ConsensusBuilder>
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<IdentityThreshold>0.9</IdentityThreshold>
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<CoverageThreshold>0</CoverageThreshold>
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<MinIntersectionLength>10</MinIntersectionLength>
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<MinTerminationReadsNumber>1</MinTerminationReadsNumber>
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<Reassembler>
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<IdentityThreshold>0.9</IdentityThreshold>
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<MinTerminatingSequenceCoverage>0</MinTerminatingSequenceCoverage>
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<PairReadTerminationThreshold>0.1</PairReadTerminationThreshold>
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<MinReadLength>50</MinReadLength>
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</Reassembler>
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<Debug>false</Debug>
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</ConsensusBuilder>
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<Postprocessor>
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<Enabled>true</Enabled>
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<MinFragmentLength>500</MinFragmentLength>
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<MinIdentity>0.99</MinIdentity>
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<MinFragmentCoverage>0.99</MinFragmentCoverage>
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<Debug>false</Debug>
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</Postprocessor>
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</config>

‎libs/virgena/config_test_linux.xml

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<config>
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<Data>
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<pathToReads1>./data/mix.01_AE.B.C_100000_p1.fastq.gz</pathToReads1>
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<pathToReads2>./data/mix.01_AE.B.C_100000_p2.fastq.gz</pathToReads2>
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<InsertionLength>1000</InsertionLength>
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</Data>
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<Reference>./data/HXB2.fasta</Reference>
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<OutPath>./res/</OutPath>
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<ThreadNumber>-1</ThreadNumber>
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<BatchSize>1000</BatchSize>
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<ReferenceSelector>
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<Enabled>true</Enabled>
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<UseMajor>false</UseMajor>
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<ReferenceMSA>./data/HIV_RefSet_msa.fasta</ReferenceMSA>
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<PathToVsearch>./tools/vsearch</PathToVsearch>
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<UclustIdentity>0.95</UclustIdentity>
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<MinReadLength>50</MinReadLength>
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<MinContigLength>1000</MinContigLength>
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<Delta>0.05</Delta>
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<MaxNongreedyComponentNumber>5</MaxNongreedyComponentNumber>
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<MapperToMSA>
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<K>7</K>
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<IndelToleranceThreshold>1.5</IndelToleranceThreshold>
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<pValue>0.01</pValue>
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<RandomModelParameters>
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<Order>4</Order>
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<ReadNum>1000</ReadNum>
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<Step>10</Step>
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</RandomModelParameters>
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</MapperToMSA>
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<Graph>
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<MinReadNumber>5</MinReadNumber>
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<VertexWeight>10</VertexWeight>
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<SimilarityThreshold>0.5</SimilarityThreshold>
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<Debug>false</Debug>
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</Graph>
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<Debug>false</Debug>
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</ReferenceSelector>
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<Mapper>
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<K>5</K>
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<IndelToleranceThreshold>1.25</IndelToleranceThreshold>
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<pValue>0.01</pValue>
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<RandomModelParameters>
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<Order>4</Order>
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<ReadNum>1000</ReadNum>
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<Step>10</Step>
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</RandomModelParameters>
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<Aligner>
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<Match>2</Match>
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<Mismatch>-3</Mismatch>
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<GapOpenPenalty>5</GapOpenPenalty>
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<GapExtensionPenalty>2</GapExtensionPenalty>
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</Aligner>
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</Mapper>
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<ConsensusBuilder>
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<IdentityThreshold>0.9</IdentityThreshold>
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<CoverageThreshold>0</CoverageThreshold>
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<MinIntersectionLength>10</MinIntersectionLength>
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<MinTerminationReadsNumber>1</MinTerminationReadsNumber>
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<Reassembler>
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<IdentityThreshold>0.9</IdentityThreshold>
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<MinTerminatingSequenceCoverage>0</MinTerminatingSequenceCoverage>
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<PairReadTerminationThreshold>0.1</PairReadTerminationThreshold>
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<MinReadLength>50</MinReadLength>
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</Reassembler>
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<Debug>false</Debug>
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</ConsensusBuilder>
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<Postprocessor>
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<Enabled>true</Enabled>
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<MinFragmentLength>500</MinFragmentLength>
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<MinIdentity>0.99</MinIdentity>
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<MinFragmentCoverage>0.99</MinFragmentCoverage>
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<Debug>false</Debug>
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</Postprocessor>
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</config>

‎libs/virgena/config_test_win.xml

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<config>
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<Data>
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<pathToReads1>./data/mix.01_AE.B.C_100000_p1.fastq.gz</pathToReads1>
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<pathToReads2>./data/mix.01_AE.B.C_100000_p2.fastq.gz</pathToReads2>
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<InsertionLength>1000</InsertionLength>
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</Data>
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<Reference>./data/HXB2.fasta</Reference>
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<OutPath>./res/</OutPath>
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<ThreadNumber>-1</ThreadNumber>
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<BatchSize>1000</BatchSize>
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<ReferenceSelector>
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<Enabled>true</Enabled>
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<UseMajor>false</UseMajor>
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<ReferenceMSA>./data/HIV_RefSet_msa.fasta</ReferenceMSA>
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<PathToVsearch>./tools/vsearch.exe</PathToVsearch>
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<UclustIdentity>0.95</UclustIdentity>
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<MinReadLength>50</MinReadLength>
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<MinContigLength>1000</MinContigLength>
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<Delta>0.05</Delta>
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<MaxNongreedyComponentNumber>5</MaxNongreedyComponentNumber>
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<MapperToMSA>
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<K>7</K>
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<IndelToleranceThreshold>1.5</IndelToleranceThreshold>
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<pValue>0.01</pValue>
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<RandomModelParameters>
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<Order>4</Order>
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<ReadNum>10000</ReadNum>
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<Step>10</Step>
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</RandomModelParameters>
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</MapperToMSA>
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<Graph>
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<MinReadNumber>5</MinReadNumber>
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<VertexWeight>10</VertexWeight>
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<SimilarityThreshold>0.5</SimilarityThreshold>
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<Debug>false</Debug>
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</Graph>
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<Debug>false</Debug>
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</ReferenceSelector>
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<Mapper>
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<K>5</K>
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<IndelToleranceThreshold>1.25</IndelToleranceThreshold>
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<pValue>0.01</pValue>
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<RandomModelParameters>
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<Order>4</Order>
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<ReadNum>10000</ReadNum>
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<Step>10</Step>
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</RandomModelParameters>
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<Aligner>
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<Match>2</Match>
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<Mismatch>-3</Mismatch>
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<GapOpenPenalty>5</GapOpenPenalty>
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<GapExtensionPenalty>2</GapExtensionPenalty>
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</Aligner>
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</Mapper>
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<ConsensusBuilder>
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<IdentityThreshold>0.9</IdentityThreshold>
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<CoverageThreshold>0</CoverageThreshold>
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<MinIntersectionLength>10</MinIntersectionLength>
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<MinTerminationReadsNumber>1</MinTerminationReadsNumber>
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<Reassembler>
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<IdentityThreshold>0.9</IdentityThreshold>
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<MinTerminatingSequenceCoverage>0</MinTerminatingSequenceCoverage>
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<PairReadTerminationThreshold>0.1</PairReadTerminationThreshold>
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<MinReadLength>50</MinReadLength>
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</Reassembler>
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<Debug>false</Debug>
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</ConsensusBuilder>
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<Postprocessor>
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<Enabled>true</Enabled>
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<MinFragmentLength>500</MinFragmentLength>
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<MinIdentity>0.99</MinIdentity>
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<MinFragmentCoverage>0.99</MinFragmentCoverage>
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<Debug>false</Debug>
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</Postprocessor>
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</config>

‎libs/virgena/data/HIV_RefSet_msa.fasta

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‎libs/virgena/data/HXB2.fasta

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>HXB2 Reference 1 to 9719
2+
TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA

‎libs/virgena/data/mix.01_AE.B.C_100000_p1.fastq.gz

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‎libs/virgena/data/mix.01_AE.B.C_100000_p2.fastq.gz

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‎libs/virgena/tools/vsearch

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‎libs/virgena/tools/vsearch.exe

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