Scaffolding with scaffhic:
  1 HiC pairs are aligned against the target assembly using BWA mem with a tag -5SPM for HiC reads
  2 PCR duplications and other artefacts are screened and removed from further data processing
  3 Based on read distributions, Contig Distance Index (CDI) is used to quantify the likelihood of contig joins
  4 Order and orientation are determined by pair numbers on contigs
  5 Relation matrix and partner matrix are used to reduce join errors
  6 6 iterations are carried out for genome scaffolding
  7 Contigs are arranged into a scaffolding structure
  8 Distributions of HiC insert mapping sizes are plotted as a png image file  
  9 HiC map is produced based on the scaffolded assembly

$ git clone  https://github.com/wtsi-hpag/scaffhic.git 
$ cd scaffhic
$ ./install.sh

       $ /full/path/to/scaffhic/src/scaffhic -nodes <nodes> -score <score> \
   	 -depth <depth_of_matrix> -length <contig_length> \
             -fq1 Input_read_1 -fq2 Input_read_2 draft-assembly.fasta genome-hic.fasta \
       
       Parameters:
         nodes:        number of CPUs requested  [ default = 30 ]
         depth:        number of columns of Partner Matrix [ default = 50 ]
         score:        score of Contig Distance Index (CDI) [ default CDI = 200 ]
         length:       minimum contig length considering for scaffolding [ default = 500000 ]

       $ /full/path/to/scaffhic/src/scaffhic -nodes <nodes> -score <score> \
   	 -depth <depth_of_matrix> -length <contig_length> \
             -map genome-hic.map -plot genome-hic-length.png -file 0 \ 
             -fq1 Input_read_1 -fq2 Input_read_2 genome-hic.fasta test_scaffold_file \
       
       Parameters:
         nodes:        number of CPUs requested  [ default = 30 ]
         depth:        number of columns of Partner Matrix [ default = 50 ]
         score:        score of Contig Distance Index (CDI) [ default CDI = 200 ]
         length:       minimum contig length considering for scaffolding [ default = 500000 ]

       PretextView is a desktop application for viewing pretext contact maps
       The package has different linux and Mac versions (linux version included in scaffhic)
       
   $ /full/path/to/scaffhic/src/seqbin-bin/PretextView genome-hic.map \
    
       More information, go to https://github.com/wtsi-hpag/PretextView

       $ /full/path/to/scaffhic/src/scaffhic -nodes <nodes> -score <score> \
   	 -depth <depth_of_matrix> -length <contig_length> \
             -data /full/path/to/tmp_rununik_27152/align.dat  \
             draft-assembly.fasta genome-hic.fasta \
      
       This saves alignment time and can get the results quickly. 

       $ /full/path/to/scaffhic/src/scaffhic -nodes 30 -score 200 -depth 50 -length 500000 \
             -fq1 GM12878-HiC_1.fastq.gz -fq2 GM12878-HiC_2.fastq.gz genome_assembly.fasta genome-scaffhic.fasta \
      
       $ /full/path/to/scaffhic/src/scaffhic -nodes 30 -score 200 -depth 50 -length 500000 \
             -map genome-hic.map -plot genome-hic-length.png -file 0 \
             -fq1 GM12878-HiC_1.fastq.gz -fq2 GM12878-HiC_2.fastq.gz genome-scaffhic.fasta genome-hic2.fasta \
      
       After the above two steps, You now have  
          1. Scaffolded assembly file: genome-scaffhic.fasta; 
          2. HiC map: genome-hic.map;  
          3. HiC length distribution image: genome-hic-length.png 
          4. Assembly file produced in the visualization step:  genome-hic2.fasta 
             This file is not used, but it might be slightly better than genome-scaffhic.fasta 
             The visualization results are based on genome-scaffhic.fasta 
             
      To view it on a desktop linux or Mac laptop use PretextView https://github.com/wtsi-hpag/PretextView  \
      $ ./PretextView genome-hic.map

       $ /full/path/to/scaffhic/src/breakhic -nodes <nodes> -grid <grid size> -break <break code> \
             -fq1 Input_read_1 -fq2 Input_read_2 draft-assembly.fasta break-hic.fasta \
       
           Parameters:
         nodes:        number of CPUs requested  [ default = 30 ]
         grid:         grid size to search breakpoints, the smaller, the more CPU time [ default = 100 ]
         break:        break code: 0 - no break; 1 - break on contigs and scaffolds; 2 - contig break only [ default = 1 ]

       $ /full/path/to/scaffhic/src/breakhic -nodes <nodes> -grid <grid size> \
             -break <break code> -data /full/path/to/tmp_rununik_27152/align.dat  \
             draft-assembly.fasta break-hic.fasta \
      
       This saves alignment time and can get the results quickly. 

       $ /full/path/to/scaffhic/src/breakhic -nodes 30 -grid 100 \
             -fq1 GM12878-HiC_1.fastq.gz -fq2 GM12878-HiC_2.fastq.gz genome_assembly.fasta genome-break.fasta \

       After the above step, You now have
          1. Assembly file with broken contigs: genome-break.fasta
          2. Breakpoint information file: genome-break.fasta.brk

If you have multiple paired-end fastq files   \
read1_1.fq.gz read2_1.fq.gz read3_1.fq.gz     \
read1_2.fq.gz read2_2.fq.gz read3_2.fq.gz     \

You need to do                                \
cat read1_1.fq.gz read2_1.fq.gz read3_1.fq.gz > read_1.fq.gz \
cat read1_2.fq.gz read2_2.fq.gz read3_2.fq.gz > read_2.fq.gz \ 

The final used files are read_1.fq.gz read_2.fq.gz           \

breakhic has been implemented into scaffhic and no need to run breakhic separately  \
breakhic might be useful when you run it before other scaffolding tools such as SALSA or 3dDNA \