sb2nhri Files

Patch is a solution to exploit a small amount of PacBio corrected long reads (PBcRs) to improve the off-the-shelf draft genomes assembled from short reads.

a, How to use?
 1, Docker Image 990210oliver/patch.docker 
  Use docker to pull docker image and run. 
  $ docker pull 990210oliver/patch.docker
  $ docker run [options] 990210oliver/patch.docker /bin/bash
		
 2, patch.tar.gz
  To install all related tools, and use python scripts to run. 
  -Prerequisites-
   * Linux 64-bit environment
   * Python 2.6 or higher (http://www.python.org/)
   * MUMmer 3.22 or higher (http://mummer.sourceforge.net/)
   * Blast 2.2.25+ or higher (http://blast.ncbi.nlm.nih.gov/)
   * Soap2 2.21 or higher (http://soap.genomics.org.cn/soapaligner.html)
  -Installation-
   # wget http://sourceforge.net/projects/sb2nhri/files/Patch/patch.tar.gz
   # tar zxvf patch.tar.gz
   Add patch folder to $PATH.
						
b, run patch.py (with docker)
 -example-
		
  1, E. coli K12 MG1655
   # patch.py
   Please give a config file!
   # mkdir test
   # cd test
   # wget http://sourceforge.net/projects/sb2nhri/files/Patch/examples/ecoli.tar.gz
   # tar zxvf ecoli.tar.gz
   ecoli/
   ecoli/corrected.long.fasta	(PBcRs corrected by using ECTools with Abyss's unitigs)
   ecoli/my.ctg.fasta (Assembly of ECTools + runCA)
   ecoli/myconfig
   
   # cat ecoli/myconfig
   in_ref=/test/ecoli/my.ctg.fasta
   in_clr=/test/ecoli/corrected.long.fasta
   source=/opt
   nucmer=nucmer
   makeblastdb=makeblastdb
   blastn=blastn
			
   # N50.py ecoli/my.ctg.fasta
   whole:4695577
   N50: 4644297
   Number of contigs: 12
   Length of the longest contig: 4644297
   				
   # patch.py ecoli/myconfig
   whole:4645330
   N50: 4644297
   Number of contigs: 2
   Length of the longest contig: 4644297


  2, yeast (S. cerevisiae W303)
   # mkdir test
   # cd test
   # wget http://sourceforge.net/projects/sb2nhri/files/Patch/examples/yeast.tar.gz         
   # tar zxvf yeast.tar.gz
   yeast/
   yeast/corrected.long.fasta (PBcRs corrected by using ECTools with Abyss's unitigs)
   yeast/my.ctg.fasta (Assembly of ECTools + runCA)
   yeast/myconfig
   	
   # cat yeast/myconfig
   in_ref=/test/yeast/my.ctg.fasta
   in_clr=/test/yeast/corrected.long.fasta
   source=/opt
   nucmer=nucmer
   makeblastdb=makeblastdb
   blastn=blastn
   
   # N50.py yeast/my.ctg.fasta
   whole:13221295
   N50: 476437
   Number of contigs: 115
   Length of the longest contig: 889557				
   					
   # patch.py yeast/myconfig		
   whole:12203626
   N50: 734494
   Number of contigs: 35
   Length of the longest contig: 1528116
				
c, config file

  in_ref=/path/assembly.ctg.fasta
	in_clr=/path/PBcR.fasta
	source=/path/patch
	nucmer=nucmer
	makeblastdb=makeblastdb
	blastn=blastn

       
  1, The input files of pre-assembled contigs and PacBio corrected reads (PBcRs):
   in_ref=/path/assembly.ctg.fasta
   in_clr=/path/PBcR.fasta
		
  2, The path of Patch: 
   source=/path/patch
		
  3, The paths of tools required by Patch
   nucmer=/path/nucmer
   makeblastdb=/path/makeblastdb
   blastn=/path/blastn
		
[Option]
  4, If the genome size was specified in the config file, the longest 15X PBcRs are selected and saved as my_CLR.fa.Long.fa:
   clrdepth=15 
   (default:15)
   genome_size=4650000

  5, Soap2 is required for read mapping:
   2bwt-builder=/path/2bwt-builder
   soap=/path/soap

  6, A threshold of coverage(depth), to split contig at zero coverage:
   depth=0 
   (default:0, available range: 0-5)

  7, The paths of short reads and the range of insert size, no inset is required for single-end library:
   read1=/path/read1.fa or fq
   read2=/path/read1.fa or fq
   min_i=100(default:100)
   max_i=200(default:200) 
    		
Date: 2015/10/13 
Author: Yu-Chieh Liao (jade@nhri.org.tw) and Hsin-Hung Lin (oliver0618@nhri.org.tw)