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Citations per year

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Platanus specifications

Information


Unique identifier OMICS_03830
Name Platanus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • BactSNP
  • Platanus assembler
  • Platanus_trim
  • Platanus-allee

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Publication for Platanus

Platanus in pipelines

 (19)
2018
PMCID: 5872505
PMID: 29587653
DOI: 10.1186/s12863-018-0603-1

[…] analysis. subsequent quality trimming (q > 30) and artificial sequence elimination steps were achieved manually. the cleaned reads were subjected to build l. racemosus genome contigs utilizing platanus software (v1.2.4) []. assemblies with variable k-mers (27, 29, 31, 33, 35, and 37) were conducted in parallel, and the resultants were merged into l. racemosus genome scaffolds of unique […]

2017
PMCID: 5388864
PMID: 28401893
DOI: 10.1038/srep46151

[…] removed using a combination of bowtie and prinseq against the genome reference consortium human build 38 (hg38) assembly. phage genomes were assembled using spades genome assembler and verified on a platanus assembler which generated 1 complete contig per genome. genome annotation was done using dna master. this program concurrently runs a collection of programs, including glimmer v. 3.02 […]

2017
PMCID: 5491122
PMID: 28662104
DOI: 10.1371/journal.pone.0180053

[…] library preparing using the nextera xt dna library preparation kit for v. aphrogenes and truseq pcr-free kit for v. algivorus, v. casei and v. rumoiensis. the genome sequence was assembled using platanus []. the sequence was deposited in the ddbj/genbank/embl database under accession numbers described below., sequences of eight protein-coding genes (ftsz, gapa, gyrb, mreb, pyrh, reca, rpoa, […]

2017
PMCID: 5510158
PMID: 28748134
DOI: 10.12938/bmfh.16-026

[…] whole-genome sequencing using a 300-bp pair-end illumina miseq system yielded 5,829,866 reads, which corresponds to approximately 700-fold coverage. de novo assembly was performed using the platanus_b assembler (version 1.1.0) with the default settings after preprocessing the raw reads to remove low-quality bases and adapter sequences using platanus_trim (version 1.0.7) []. the draft […]

2017
PMCID: 5637492
PMID: 29025932
DOI: 10.1128/genomeA.01030-17

[…] h. akashiwo ptdna of nies293 (eu168190) and ccmp452 (eu168191) (), using burrows-wheeler alignment software. the mapped reads were extracted using samtools software and assembled using the platanus software (). the obtained contigs were aligned with the reference sequences, and the corresponding segments in the references were replaced with the contigs. the process was repeated […]


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Platanus in publications

 (79)
PMCID: 5906075
PMID: 29675466
DOI: 10.1126/sciadv.aao5416

[…] to detect highly differentiated mimetic genomic regions from the nonmimetic ones, each raw mimetic scaffold was divided into nonoverlapping 50-kb segments, and these segments were aligned to the raw platanus scaffolds of the nonmimetic (aa) individual, using blat (version 36) () with the following options: “-minidentity=70 -maxintron=50000.” from raw output of blat (psl format), […]

PMCID: 5901865
PMID: 29661185
DOI: 10.1186/s12915-018-0509-4

[…] libraries, before and after read trimming, are listed in additional file : table s1., de novo genome assembly and scaffolding employing the processed short reads were carried out using the program platanus v1.2.1 [] with its default parameters. the assembly step employed paired-end reads as well as singletons whose pairs were filtered, and the scaffolding step employed paired-end and mate-pair […]

PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] genome from illumina paired-end reads as follows: we trimmed adapters with trimmomatic v0.32 [], performed error-correction with allpaths-lg version 44,837 [] and assembled the processed reads using platanus version 1.2.1 (with default parameters except k = 48) []. we created a coding-region training set using the jgi genome annotations of nematostella vectensis v1.0 [] and then used augustus […]

PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] 69, the estimated genome size was calculated to be 885.29 mb (table ) and the estimated repeat sequencing ratio was 33.74%., all the pair-end illumina reads were first assembled into scaffolds using platanus_v1.2.4 (platanus, rrid:scr_015531) [], and the gaps were then filled by gapcloser_v1.12-r6 (gapcloser, rrid:scr_015026) []. subsequently, the pacbio data were used for additional gap filling […]

PMCID: 5896239
PMID: 29785397
DOI: 10.1155/2018/7984292

[…] 0.32) []. we assembled the paired-end short read sequences using soapdenovo2 assembly software [], mapped the resulting contigs to the mate pair read sequences, and closed gaps between contigs with platanus []. then, we converted the mate pair sequences to reverse complemental sequences using the reverse complement tool in the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). […]


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Platanus institution(s)
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan

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