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collapse_rescue

Method for rescuing collapsed contigs.

Installation

  • install collapse_rescue 
    git clone https://github.com/wangyibin/collapse_rescue.git
cd collapse_rescue
chmod +x bin/* 
pip install -r requirements.txt
  • configure
    vim ~/.bash_profile 
    export PATH=$HOME/software/collapse_rescue/bin:$PATH
export PATH=$HOME/software/ALLHiC_adjuster/bin:$PATH
export PATH=$HOME/software/ALLHiC/bin:$PATH
export PATH=$HOME/software/popCNV/bin:$PATH

Dependencies

  1. python packages

    • rich
    • joblib
    • numpy
    • pandas
    • pyfaidx
    • pytools

  2. softwares

Methods

  1. calculate the copy number of each contig using popCNV 
    mkdir read_depth && cd read_depth
mosdepth -t 10 -b 1000 LAp LAp.contig.bam
cd ..
popCNV -g LAp.contig.fasta -s 1000 -r read_depth/ -b bamfile/ -l contig.bed -w wrk_dir --group group.list  --sample sample.list --wild 0 -t 10
    Alignment must use contig-level assembly as reference.
  2. rescue 
    agp2cluster.py LAp.agp > LAp.clusters.txt
dup_collapsed_contigs.py Allele.ctg.table 06.genes.round.cn LAp.clusters.txt 8 -o output
    Allele.ctg.table generated from ALLHiC
    06.genes.round.cn generated from popCNV
  3. optimize 
    convert_agp_to_tour.py LAp.agp tour
dup_collapsed_optimize.py collapsed.rescued.txt LAp.pairs.txt LAp.clm tour -o new_tour > collapsed.optimize.txt
    LAp.pairs.txt and LAp.clm were generated from allhic extract
  4. build 
    dup_collapsed_fasta.py collapsed.optimize.txt LAp.contig.fasta > contig.dup.fasta
cd new_tour
ALLHiC_build contig.dup.fasta
    Results are the groups.agp and groups.asm.fasta.
    Sequences ID with _d are the collapsed contigs.

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