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# Content
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# Function modularization
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Workflow modularization and function mapping |
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An overview of the precise changes for modularization of the original PopIns/PopIns2 functions in the new Popins4snake including documentation of the new functions.
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\ No newline at end of file |
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## PopIns/PopIns2 functions to Popins4snake functions
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PopIns2_assemble ---> Popins4snake_crop-unmapped
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---> SAMTOOLS SORT
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---> SICKLE filtering
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---> MINIA or Velvet assembler
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PopIns2_merge-contigs ---> Popins4snake_merge-contigs
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---> BWA index
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PopIns2_contigmap ---> map_supercontigs (BWA mem)
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---> SAMTOOLS SORT
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---> Popins4snake_merge-bams
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---> SAMTOOLS SORT
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---> SAMTOOLS INDEX
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---> Popins4snake_find-locations
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---> Popins4snake_merge-locations
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PopIns2_place ---> No change
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PopIns2_genotype ---> bcftools view&sort
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---> genotype
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---> bcftools merge |
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\ No newline at end of file |
