HicTrioBinning

A multithread pipeline to bin Hi-C reads for trios.

RED: Input, YELLOW: this pipeline, GREEN: Output

• Instruction:

  Input:

  1. two haplotype-resolved assembled contigs
  2. Hi-C reads of the child

Output:

    two haplotype-resolved Hi-C read sets for Hi-C assembly

Dependencies:

    1. BWA 

bwa github

    2. Seqtk

seqtk github

Usage:

    /usr/bin/bash HTB.sh -M Input_MAT_conitg.fasta -P Input_PAT_contig.fasta \
    -1 Input_Hi-C_R1.fq.gz -2 Input_Hi-C_R2.fq.gz -N 10 -B /path/to/bwa \
    -S /path/to/seqtk -O /path/to/output/ -I 1

Option:

    -I < bwa indices of haplotype assemblies: 1|0 > 
    -M < input draft maternal-specific haplotype assembly of the child > 
    -P < input draft paternal-specific haplotype assembly of the child > 
    -1 < hybrid Hi-C Reads R1 of the child > 
    -2 < hybrid Hi-C Reads R2 of the child > 
    -N < thread number : 20 (default) > 
    -B < path to installed bwa > 
    -S < path to installed seqtk > 
    -O < /path/to/output >
    -h <help> 

example CMD line:

• Please set -I to 1 if you donot have bwa indices of the two haplotype assemblies.

  /usr/bin/bash HTB.sh -M Input_MAT_conitg.fasta -P Input_PAT_contig.fasta -1 Input_Hi-C_R1.fq.gz -2 Input_Hi-C_R2.fq.gz -N 10 -B /share/app/bwa-0.7.12/bwa -S /share/app/seqtk/1.3/seqtk -O /path/to/output/ -I 1 

• Please set -I to 0 if you already have bwa indices of the two haplotype assemblies.

  /usr/bin/bash HTB.sh -M Input_MAT_conitg.fasta -P Input_PAT_contig.fasta -1 Input_Hi-C_R1.fq.gz -2 Input_Hi-C_R2.fq.gz -N 10 -B /share/app/bwa-0.7.12/bwa -S /share/app/seqtk/1.3/seqtk -O /path/to/output/ -I 0