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init. v1.2.2, which is used for paper submission.
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‎LICENSE‎

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‎Makefile‎

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CXX = g++
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MAIN = meta_platanus.pl
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SUBDIRS = src/minimap2 src/meta_platanus src/meta_platanus_phase src/megahit src/samtools src/bwa
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SUBBIN = sub_bin
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.PHONY:all clean $(SUBDIRS) $(SUBBIN)
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all: $(MAIN) $(SUBDIRS) $(SUBBIN)
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$(MAIN):
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src/samtools:
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cd src/samtools && ./configure
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$(SUBDIRS):
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$(MAKE) -C $@
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$(SUBBIN):
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mkdir -p $(SUBBIN)
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cp src/meta_platanus/meta_platanus $(SUBBIN)
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cp src/meta_platanus_phase/meta_platanus_phase $(SUBBIN)
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cp src/minimap2/minimap2 $(SUBBIN)
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cp src/megahit/megahit* $(SUBBIN)
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cp src/samtools/samtools $(SUBBIN)
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cp src/bwa/bwa $(SUBBIN)
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cp src/scripts/*.pl src/scripts/*.pm $(SUBBIN)
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cp pre_built_bin/metabat/metabat2 $(SUBBIN)
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cp pre_built_bin/metabat/jgi_summarize_bam_contig_depths $(SUBBIN)
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clean:
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rm -rf $(SUBBIN)
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cd src/meta_platanus && make clean
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cd src/meta_platanus_phase && make clean
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cd src/minimap2 && make clean
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cd src/megahit && make clean
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cd src/samtools && make clean
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cd src/bwa&& make clean
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# $(MAKE) clean -C $(SUBDIRS)

‎README.md‎

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# MetaPlatanus README.md
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## Description
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MetaPlatanus is a de novo assembler for metagenome (microbiome). The features of this tool are as follows:
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(1) It can utilize various types of long-range information such as mate-pairs (jumping libraries), Oxford-Nanopore/PacBio long reads and 10x linked reads (barcoded reads).
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(2) Coverage depths, k-mer frequencies and results of the binning tool are also employed to extend sequences and correct mis-assemblies.
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(3) Contig-assembly, scaffolding, gap-closing and binning are automatically executed at once.
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(4) As the other mode, haplotypes (strain genomes) in a metagenome can be distinguished and constructed.
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(5) MetaPlatanus requires at least one short-read paired-end library.
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## Version
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v1.2.2
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## Web site
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<http://platanus.bio.titech.ac.jp/>
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## Author
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Rei Kajitani at Tokyo Institute of Technology wrote key source codes.
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Address for this tool: <platanus@bio.titech.ac.jp>
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## Dependency (the tools below are included in this package)
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* Minimap2
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- <https://github.com/lh3/minimap2>
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- Only required to use Oxford-Nanopore/PacBio long reads.
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- v2.17-r943
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* BWA
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- <http://bio-bwa.sourceforge.net/>
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- v0.7.17-r1194
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* MEGAHIT
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- <https://github.com/voutcn/megahit>
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- v1.1.3
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* MetaBAT2
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- <https://bitbucket.org/berkeleylab/metabat>
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- v2.12.1
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* SAMtools
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- <http://www.htslib.org/>
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- v1.3.1
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## Installation
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Currently MetaPlatanus can be executed in Linux.
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To compile (build), just type "make".
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```
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make
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```
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The main program is "meta_platanus.pl".
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Note that the directory "sub_bin", which consists of Perl-scripts and other tools, should be specified (-sub_bin option) or put in the same directory of meta_platanus.pl.
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There are four ways to execute meta_platanus.pl.
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Below, "build-directory" means the directory where you typed "make" and it consists of meta_platanus.pl and sub_bin.
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(1) Directly type the path to build meta_platanus.pl.
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```
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/build-directory/mata_platanus.pl ...
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```
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(2) Add the build-directory to PATH.
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```
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export PATH=/build-directory/:$PATH
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meta_platanus.pl ...
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```
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(3) Copy meta_platanus.pl and sub_bin to a directory listed in PATH (e.g. $HOME/bin).
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```
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cp -r sub_bin meta_platanus.pl $HOME/bin
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meta_platanus.pl ...
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```
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(3) Copy meta_platanus.pl to a directory listed in PATH, and use the "-sub_bin" option.
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```
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cp meta_platanus.pl $HOME/bin
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meta_platanus.pl [command] -sub_bin /build-directory/sub_bin ...
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```
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## Synopsis of consensus assembly
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### Inputs
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* Illumina paired-end: PE_1.fq PE_2.fq (mandatory)
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* Illumina mate-pair: MP_1.fq MP_2.fq (optional)
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* Oxford Nanopor long-reads: ONT.fq (optional)
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### Commands
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```
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meta_platanus.pl cons_asm -IP1 PE_1.fq PE_2.fq -OP2 MP_1.fq MP_2.fq -ont ONT.fq >log.txt 2>&1
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```
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### Final output
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out_finalClusters_all.fa
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out_finalClusters (directory)
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## Synopsis of haplotype-phasing assembly
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### Inputs
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* Illumina paired-end: PE_1.fq PE_2.fq (mandatory)
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* Illumina mate-pair: MP_1.fq MP_2.fq (optional)
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* Oxford Nanopor long-reads: ONT.fq (optional)
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### Commands
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```
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meta_platanus.pl phase_asm -IP1 PE_1.fq PE_2.fq -OP2 MP_1.fq MP_2.fq -ont ONT.fq >log.txt 2>&1
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```
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### Final output
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out_allPhasedBlock.fa (including sequences below)
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out_primaryBubble.fa
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out_secondaryBubble.fa
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out_nonBubbleOther.fa
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...
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---
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## Consensus assembly usage
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### Command
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```
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meta_platanus.pl cons_asm -IP1 short_R1.fastq(a) short_R2.fastq(a) [Options] ...
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```
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### Options
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```
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-IP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id inward_pair_files (reads in 2 files, fasta or fastq; at least one library required)
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-OP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id outward_pair_files (reads in 2 files, fasta or fastq; aka mate-pairs or jumping-library)
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-binning_IP{INT} FWD1 REV1 ... : lib_id inward_pair_files for binning process. (reads in 2 files, fasta or fastq; the data are usually from another sample)
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-p FILE1 [FILE2 ...] : PacBio long-read file (fasta or fastq)
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-ont FILE1 [FILE2 ...] : Oxford Nanopore long-read file (fasta or fastq)
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-x PAIR1 [PAIR2 ...] : barcoded_pair_files (10x Genomics) (reads in 1 file, interleaved, fasta or fastq)
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-X FWD1 REV1 [FWD2 REV2 ...] : barcoded_pair_files (10x Genomics) (reads in 2 files, fasta or fastq)
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-t INT : number of threads (<= 1; default, 1)
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-m INT : memory limit for making kmer distribution (unit, GB; default, 0.75 * available_memory))
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-o STR : prefix of output files (default "out")
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-tmp DIR : directory for temporary files (default, ".")
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-sub_bin DIR : directory for sub-executables, such as mata_plantaus and minimap2 (default, directory-of-this-script/sub_bin)
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-megahit_min_len : minimum length of contigs of MEGAHIT (default, 500)
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-overwrite : overwrite the previous results, not re-start (default, off)
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-h, -help : display usage
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```
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### Outputs:
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PREFIX_finalClusters_all.fa
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PREFIX_finalClusters (directory
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PREFIX is specified by -o
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## Assemble each haplotype in a metanogme (phasing)
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### Command
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```sh
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meta_platanus.pl phase_asm -IP1 short_R1.fastq(a) short_R2.fastq(a) [Options] ...
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```
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### Options
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```
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-IP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id inward_pair_files (reads in 2 files, fasta or fastq; at least one library required)
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-OP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id outward_pair_files (reads in 2 files, fasta or fastq; aka mate-pairs or jumping-library)
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-p FILE1 [FILE2 ...] : PacBio long-read file (fasta or fastq)
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-ont FILE1 [FILE2 ...] : Oxford Nanopore long-read file (fasta or fastq)
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-x PAIR1 [PAIR2 ...] : barcoded_pair_files (10x Genomics) (reads in 1 file, interleaved, fasta or fastq)
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-X FWD1 REV1 [FWD2 REV2 ...] : barcoded_pair_files (10x Genomics) (reads in 2 files, fasta or fastq)
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-t INT : number of threads (<= 1; default, 1)
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-m INT : memory limit for making kmer distribution (unit, GB; default, 0.75 * available_memory))
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-o STR : prefix of output files (default "out")
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-tmp DIR : directory for temporary files (default, ".")
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-sub_bin DIR : directory for sub-executables, such as mata_plantaus and minimap2 (default, directory-of-this-script/sub_bin)
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-overwrite : overwrite the previous results, not re-start (default, off)
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-h, -help : display usage
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```
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### Outputs:
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```
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PREFIX_allPhasedBlock.fa (including sequences below)
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PREFIX_primaryBubble.fa
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PREFIX_secondaryBubble.fa
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PREFIX_nonBubbleOther.fa
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...
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```
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PREFIX is specified by -o
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---
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## Notes
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* Options related to run time
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Although -t (number of threads) of all commands and -m (memory amount) of the "assemble" command are
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not mandatory to run, it is recommended to set the values adjusting your machine-environment.
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These options may severely effect the run time.
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e.g.,
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Available number of threads and memory amount are 4 and 16GB, respectively.
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-> -t 4 -m 16
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* Paired-end (mate-pair) input
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The "phase" and "consensus" accept paired-end and/or mate-pair libraries. Paired libraries are
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classified into "inward-pair" and "outward-pair" according to the sequence direction.
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For file formats, separate and interleaved files can be input through -IP (-OP) and -ip (-op)
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options, respectively.
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Inward-pair (usually called "paired-end", accepted in options "-IP" or "-ip"):
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FWD --->
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5' -------------------- 3'
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3' -------------------- 5'
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<--- REV
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Outward-pair (usually called "mate-pair", accepted in options "-OP" or "-op"):
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---> REV
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5' -------------------- 3'
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3' -------------------- 5'
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FWD <---
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Example inputs:
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Inward-pair (separate, insert=300) : PE300_1.fq PE300_2.fq
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Outward-pair (separate, insert=2k) : MP2k_1.fa MP2k_2.fq
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Corresponding options:
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-IP1 PE300_1_pair.fq PE300_2.fq \
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-OP2 MP2k_1.fq MP2k_2.fq
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To utilize multiple-samples data, MetaPlatanus can accept the short-reads
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that exclusivelly used for the binning process through -binning-IP# options.
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e.g.,
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```
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meta_platanus.pl cons_asm \
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-IP1 sample1_R1.fq sample1_R2.fq \
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-binning_IP1 sample1_R1.fq sample1_R2.fq \
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-binning_IP2 sample2_R1.fq sample2_R2.fq \
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-binning_IP3 sample3_R1.fq sample3_R2.fq \
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...
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```

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