MetaPlatanus is a de novo assembler for metagenome (microbiome). The features of this tool are as follows: (1) It can utilize various types of long-range information such as Oxford-Nanopore/PacBio long reads, mate-pairs (jumping libraries), and 10x linked reads (experimental). (2) Coverage depths, k-mer frequencies and results of the binning tool are also employed to extend sequences and correct mis-assemblies, reducing inter-species misassemblies. (3) Contig-assembly, scaffolding, gap-closing and binning are automatically executed at once. (4) MetaPlatanus requires at least one short-read paired-end library.
v1.3.1
https://github.com/rkajitani/MetaPlatanus
http://platanus.bio.titech.ac.jp
Rei Kajitani at Tokyo Institute of Technology wrote key source codes.
Address for this tool: platanus@bio.titech.ac.jp
Currently MetaPlatanus can be executed in Linux. There are three ways.
MetaPlatanus is registered in Bioconda channel; Linux only.
conda install -c conda-forge -c bioconda metaplatanusFor any OS if Docker is available.
docker pull rkajitani/metaplatanus
# Start a container interactively,
docker run -it -v $(pwd):/work -w /work rkajitani/metaplatanus
# or run metaplatanus in one command
docker run -v $(pwd):/work -w /work --rm rkajitani/metaplatanus metaplatanus ...Install the dependencies above. If the following commands are available, you will be able to run metaplatanus.
Compile (make), and copy metaplatanus and sub_bin to a directory listed in PATH (e.g. $HOME/bin).
make
cp -r sub_bin metaplatanus $HOME/binThe main program is "metaplatanus". 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 metaplatanus. There are two ways to install metaplatanus.
metaplatanus -t 8 -m 64 -IP1 PE_1.fq PE_2.fq -ont ONT.fq >log.txt 2>&1
# num_threads, 8; memory_limit, 64GBThe files below in out_result (directory). The prefix "out" can be changed using "-o" option.
Minimap2
BWA
MetaBAT2
SAMtools
SeqKit
MEGAHIT
TGS-GapCloser (optional)
Racon (optional)
NextPolish (optional)
metaplatanus -IP1 short_R1.fastq(a) short_R2.fastq(a) [Options] ...-IP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id inward_pair_files (reads in 2 files, fasta or fastq; at least one library required)
-OP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id outward_pair_files (reads in 2 files, fasta or fastq; aka mate-pairs or jumping-library)
-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)
-p FILE1 [FILE2 ...] : PacBio long-read file (fasta or fastq)
-ont FILE1 [FILE2 ...] : Oxford Nanopore long-read file (fasta or fastq)
-x PAIR1 [PAIR2 ...] : barcoded_pair_files (10x Genomics) (reads in 1 file, interleaved, fasta or fastq)
-X FWD1 REV1 [FWD2 REV2 ...] : barcoded_pair_files (10x Genomics) (reads in 2 files, fasta or fastq)
-t INT : number of threads (<= 1; default, 1)
-m INT : memory limit for making kmer distribution (unit, GB; default, 64)
-o STR : prefix of output files (default "out")
-tmp DIR : directory for temporary files (default, ".")
-sub_bin DIR : directory for sub-executables, such as mata_plantaus and minimap2 (default, directory-of-this-script/sub_bin)
-min_cov_contig INT : k-mer coverage cutoff for contig-assembly of MetaPlatanus (default, 4 with MEGAHIT, 2 otherwise)
-min_map_idt_binning FLOAT : minimum identity (%) in read mapping for binning (default, 97)
-no_megahit : do not perfom MEGAHIT (default, off)
-no_binning : do not perfom binning (default, off)
-no_re_scaffold : do not perfom re-scaffolding (default, off)
-no_tgsgapcloser : do not use TGS-GapCloser and NextPolish (default, off)
-no_nextpolish : do not use NextPolish (default, off)
-overwrite : overwrite the previous results, not re-start (default, off)
-h, -help : display usage
-v, -version : display version PREFIX_result (directory)PREFIX is specified by -o
Kajitani, R., Noguchi, H., Gotoh, Y., Ogura, Y., Yoshimura, D., Okuno, M., Toyoda, A., Kuwahara, T., Hayashi, T. and Itoh, T. (2021) MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features. Nucleic Acids Research, gkab831. https://doi.org/10.1093/nar/gkab831
Options related to run time
Although -t (number of threads) of all commands and -m (memory amount) of the "assemble" command are
not mandatory to run, it is recommended to set the values adjusting your machine-environment.
These options may severely effect the run time.
e.g.,
Available number of threads and memory amount are 4 and 16GB, respectively.
-> -t 4 -m 16
Paired-end (mate-pair) input
The "phase" and "consensus" accept paired-end and/or mate-pair libraries. Paired libraries are
classified into "inward-pair" and "outward-pair" according to the sequence direction.
For file formats, separate and interleaved files can be input through -IP (-OP) and -ip (-op)
options, respectively.
Inward-pair (usually called "paired-end", accepted in options "-IP" or "-ip"):
FWD --->
5' -------------------- 3'
3' -------------------- 5'
<--- REV Outward-pair (usually called "mate-pair", accepted in options "-OP" or "-op"):
---> REV
5' -------------------- 3'
3' -------------------- 5'
FWD <---Example inputs:
Inward-pair (separate, insert=300) : PE300_1.fq PE300_2.fq
Outward-pair (separate, insert=2k) : MP2k_1.fa MP2k_2.fqCorresponding options:
-IP1 PE300_1_pair.fq PE300_2.fq \
-OP2 MP2k_1.fq MP2k_2.fqTo utilize multiple-samples data, MetaPlatanus can accept the short-reads that exclusivelly used for the binning process through -binning-IP# options. e.g.,
metaplatanus \
-IP1 sample1_R1.fq sample1_R2.fq \
-binning_IP1 sample1_R1.fq sample1_R2.fq \
-binning_IP2 sample2_R1.fq sample2_R2.fq \
-binning_IP3 sample3_R1.fq sample3_R2.fq \
...