Method for rescuing collapsed contigs.

• 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

1. python packages

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

2. softwares

   • ALLHiC
   • ALLHiC_adjuster
   • popCNV

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.