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