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Brief instruction for package phacro:

This is the first release v1.0 of package phacro. All the programs used for analyzing the oocyte single cell sequencing data are shown in this package, which are written in either perl or C++ computer language. The perl programs are packaged into a tar-ball "perl-scripts", while the C++ source code of each core program are packaged seperately. The pipeline programs as well as the invoked core programs are listed below: 

#1. mapping the sequencing reads to human reference genome

 reads_mapping_oocyte_pipeline.pl     the pipeline 
 bwa/samtools                         public software, http://bio-bwa.sourceforge.net/
                                                       http://samtools.sourceforge.net/
 trim_malbac_adapter_lowqual          core program to trim contaminated adapters and primers in the reads
                                      codes stored in tar-ball "clean_malbac_reads"

#2. genotype calling for each oocyte cell and heterozygous SNP calling for the donor
 
 snp_calling_oocyte_pipeline_part1.pl    the pipeline for genotype calling of each oocyte cell
 snp_calling_oocyte_pipeline_part2.pl    the pipeline for heterozygous SNP calling of the donor
 gametesnp                               core program to calculate the genotype likelihoods
                                         codes stored in tar-ball "gamete_snp_calling"  

#3. phasing the donor's haplotype with her haploid oocyte cells
  
  hetsnp_phasing_oocyte_pipeline.pl      the pipeline, phasing by dynamic programming algorithm  
  phasing_by_pairwise_hmm.pl             the pipeline, phasing by inferring pairwise crossovers and merging SNPs
  pairwisehmm                            core program, identify pairwise crossovers by hidden markov model
                                         codes stored in tar-ball "crossover_hmm"  

#4. infer crossover positions on each sequenced oocyte cell
  
  crossover_inferring_oocyte_pipeline.pl    the pipeline, infering crossover positions on each cell 
  cohmm                                     core program, infer crossover positions by hidden markov model
                                            codes stored in tar-ball "crossover_hmm"  

#5. infer chromosome copy number and identify aneuploidy in oocytes
  
  aneuploidy_normalization_factor_HMM.pl   the pipeline, generate the normalization factor file
  infer_aneuploidy_HMM_pipeline.pl         the pipeline, infer aneuploidy on the oocyte cells
  cnvhmm                                   core program, infer copy number by Hidden Markov Model
                                           codes stored in tar-ball "chr_cnv_hmm"

#6. draw the figures for oocyte cells include haplotype, crossover and aneuploidy information
 
 haplotype_drawing_pipeline_figures.pl    the pipeline, draw figures for manual curation 


The detailed instructions and usage of each program can be found by running the program with option "--help" or "-h". More details about the algorithms are described in the oocyte single cell sequencing paper as well as the related reference papers. 

Published paper: (will come out soon)
Title: Probing the Genomes of Single Human Oocytes.

If you have other questions or meet problems, please contact: Fanwei; Email: fanwei@pku.edu.cn ; 
Address: Biodynamic Optical Imaging Center, Peking University. 

Any suggestions are welcome to improve phacro! Thanks very much for your attention and support!
Source: ReadMe.txt, updated 2013-10-12