Platanus protocols

View
settings
Platanus computational protocol

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

Versioning


Add your version

Publication for Platanus

Platanus IN pipelines

 (8)
2017
PMCID: 5648229
PMID: 29049400
DOI: 10.1371/journal.pone.0186800

[…] using kod fx neo (toyobo, osaka, japan). paired-end (2 × 250 bp or 2 × 300 bp) sequencing was performed using miseq (illumina)., paired-end fastq files were used for de novo assembly using the platanus trimming tool-1.0.7 and platanus_assmbler-1.2.4 [20], and their quality was evaluated using quast 4.3 [21]. contig sequences including the dr region were selected from gap-closed fasta […]

2017
PMCID: 5648229
PMID: 29049400
DOI: 10.1371/journal.pone.0186800

[…] japan). paired-end (2 × 250 bp or 2 × 300 bp) sequencing was performed using miseq (illumina)., paired-end fastq files were used for de novo assembly using the platanus trimming tool-1.0.7 and platanus_assmbler-1.2.4 [20], and their quality was evaluated using quast 4.3 [21]. contig sequences including the dr region were selected from gap-closed fasta files, and alignment of the spacers […]

2016
PMCID: 4848470
PMID: 27120974
DOI: 10.1038/srep24863

[…] the ends of both reads, jellyfish45 to obtain k-mer frequencies in all the libraries, and quake46 to correct sequencing errors. the data processing resulted in seven libraries that were supplied to platanus47 for genome assembly: 250 bp and 500 bp paired-end libraries, 2 kbp, 6kbp, 15k bp true mate pair libraries, a library containing all the paired-end reads from the mate pair libraries, […]

2016
PMCID: 4894063
PMID: 26951782
DOI: 10.1093/gbe/evw045

[…] libraries (supplementary fig. s1, supplementary material online), and quake (kelley et al. 2010) to correct sequencing errors. the data processing resulted in nine libraries that were supplied to platanus (kajitani et al. 2014) for genome assembly: 250 bp and 500 bp paired-end libraries, three paired-end and three mate pair libraries from 2, 6, and 15 kb libraries and a single-end library […]

2016
PMCID: 5105112
PMID: 27834719
DOI: 10.1128/genomeA.01279-16

[…] using a nextera xt dna sample prep kit (illumina), and 24 million reads were generated by hiseq 2500 using the 100-bp paired-end mode. reads with high-quality scores (>28) were assembled using platanus (28), yielding five high-sequence-coverage contigs (73.2, 58.5, 57.6, 41.2, and 33.2 kb) derived from hav and numerous low-coverage contigs derived from the host dna. gaps […]

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

Platanus reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Platanus