MAECI: A Tool For Generating Consensus Nanopore Sequencing Long-read Assemblies and Error Correction
Option
-fq <Input File> Input *.fq file
-path1 <Assembly Method 1> The path of assembly method/software, default: /usr/bin/canu
-path2 <Assembly Method 2> The path of assembly method/software, default: /usr/bin/flye
-path3 <Assembly Method 3> The path of assembly method/software, default: /usr/bin/wtdbg2
-path4 <Correction Method> The path of self-correction method/software, default: /usr/bin/racon
-genome_size <Estimated Genome Size> Estimated genome size, the unit is mb
-ngs_polishing <yes:1|no:0> Whether need NGS data for polishing, default: 0
-ngs_file1 <NGS Fastq file1> The ngs fastq file, such as read_1.fq.gz
-ngs_file2 <NGS Fastq file2> The ngs fastq file, such as read_2.fq.gz
-outputdir <Output Dir> The output results pathdir
-reference <Reference Genome> The reference genome of similar species
-process <Number of process used> N processes to use, default is 1
-help print HELP message
Example:
perl /mnt/nas/bioinfo/langjidong/PERL/software/Third-Generation/Pipeline/Multiple-Assembly-Integration/Multiple-Assembly-Integration.pl -fq nanopore.fq -path1 canu -path2 flye -path3 wtdbg2 -path4 racon -genome_size 1m -ngs_polishing 1 -ngs_file1 read_1.fq.gz -ngs_file2 read_2.fq.gz -outputdir ./outputdir -reference reference.fasta -process 8
Note: There are other options for assembling methods/softwares, and theoretically one method is also possible. But we suggest that should better choose at least 3 methods. If you want to change the assembly methods, please modify the command line (Line 75-87) in this script.
Contact: langjidong@hotmail.com