Name | Modified | Size | Downloads / Week |
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examples | 2015-10-13 | ||
manual of patch.pdf | 2015-10-14 | 377.1 kB | |
readme.txt | 2015-10-13 | 3.9 kB | |
patch.tar.gz | 2015-10-13 | 29.1 kB | |
Totals: 4 Items | 410.1 kB | 0 |
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)