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Last edited by Kedi Cao

Function modularization

An overview of the precise changes for modularization of the original PopIns/PopIns2 functions in the new Popins4snake including documentation of the new functions.

PopIns/PopIns2 functions to Popins4snake functions

PopIns2_assemble ---> Popins4snake_crop-unmapped

                            ---> SAMTOOLS SORT

                            ---> SICKLE filtering

                            ---> MINIA or Velvet assembler

PopIns2_merge-contigs ---> Popins4snake_merge-contigs

                                     ---> BWA index

PopIns2_contigmap ---> map_supercontigs (BWA mem)

                              ---> SAMTOOLS SORT

                              ---> Popins4snake_merge-bams

                              ---> SAMTOOLS SORT

                              ---> SAMTOOLS INDEX

                              ---> Popins4snake_find-locations

                              ---> Popins4snake_merge-locations

PopIns2_place ---> No change

PopIns2_genotype ---> bcftools view&sort

                            ---> genotype

                            ---> bcftools merge