Hi-Cluster

Hi-Cluster is an method that generate multiple MAGs (metagenome-assembled genomes) using Hi-C reads.

Usage

Hi-Cluster is composed of three scripts (link_counter.py, merge_contactfiles.py and Hi-Cluster.py) and can be devided into three steps.

step1 (link_counter.py)

this script generates contact information from samfiles.

python link_counter.py (1)samfile.sam (2)scaffolds.fa (3)cutting_site (4)outputFileName (5)minimum_length (6)scaffoldList.txt

samfile.sam       Mapping result of Hi-C reads to scaffolds. The file should be sam format.
scaffolds.fa      input fasta file of scaffolds.
cutting_site      restriction site (e.g. MluCI -> AATT).
outputFileName    output file.
minimum_length    minimum scaffold length.
scaffoldList.txt  header of samfile. (which contain only a scaffold name per line.)

step2 (merge_contactfiles.py)

this script integrates two contact files and generate a gml file which is information of proximity among scaffolds with the style of network.

python merge_contactfiles.py (1)contactFile1.txt (2)contactFile2.txt (3)outputGMLfile.gml (4)scaffoldList.txt (5) minimum_length

contactFile1      output of link_counter.py
contactFile2      output of link_counter.py
outputGMLfile     output of merge_contactfiles.py
scaffoldList.txt  header of samfile. (which contain only a scaffold name per line.)
minimum_length    minimum scaffold length.

step3 (Hi-Cluster.py)

this script creates MAGs from gml file.

python Hi-Cluster.py (1)inputGMLfile.gml (2)fastafile.fa (3)threashold (4)outputFileName

inputGMLfile.gml  input gml file
fastafile.fa      input fasta file
threashold        the smaller this threashold is set, the more strictly scaffolds are selected. (default 0.96)
outputFileName    output file name

Input file format

・scaffoldList.txt

scaffold1
scaffold2
scaffold3
   ・
   ・
   ・