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Protocols

Racon specifications

Information


Unique identifier OMICS_25714
Name Racon
Alternative name Rapid Consensus
Interface Command line interface
Restrictions to use None
Input data A set of raw backbone sequences, a set of reads, and a set of mappings between reads and backbone sequences.
Input format GFA,FASTA,FASTQ,SAM,MHAP,PAF
Operating system Unix/Linux
Programming languages C++, Perl, Python, Shell (Bash)
Computer skills Advanced
Version 0.5.0
Stability Stable
Requirements
Ubuntu
Maintained Yes

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Documentation


Maintainer


  • person_outline Mile Sikic

Publication for Rapid Consensus

Racon citations

 (18)
library_books

Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing

2018
Genome Announc
PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] ere trimmed for adapters using PoreChop version 0.2.3 and then assembled using SMARTdenovo version 1.0 (https://github.com/ruanjue/smartdenovo). Contigs obtained from the assembly were polished using Racon version 0.5.0 () and Nanopolish version 0.8.5 (). A final polish of the assembly was performed with Pilon version 1.22 using Illumina HiSeq RNA reads extracted from pure culture laboratory ferme […]

library_books

Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada

2018
Genome Announc
PMCID: 5897807
PMID: 29650575
DOI: 10.1128/genomeA.00258-18

[…] ools software suite (http://jgi.doe.gov/data-and-tools/bbtools/). Hybrid assembly of Illumina and PacBio reads was performed with Unicycler v0.4.4 (), a wrapper tool using minimap v2.5-r622-dirty (), Racon v0.5.0 (), SPAdes v3.11.1 (), and Pilon v1.22 (). Annotation of the final assemblies was done by the National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline (). Asse […]

call_split

Community led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

2018
FEMS Microbiol Lett
PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069
call_split See protocol

[…] ch et al.) using Ion PGM reads only, then with Unicycler, version v0.4.3 (Wick et al.) also using default parameters with both Ion PGM and Nanopore reads. For the latter, the genome was polished with Racon (Vaser et al.) and Pilon (Walker et al.). The quality of both assemblies was assessed with QUAST (Gurevich et al.). […]

library_books

Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

2018
Front Microbiol
PMCID: 5817080
PMID: 29491853
DOI: 10.3389/fmicb.2018.00193

[…] he hybrid assembler Unicycler (v. 0.4.1, ). The genome bins of the two contaminating organisms were assembled from the Nanopore reads using Miniasm () and polished twice with the Nanopore reads using Racon (). No other microbe, encoding genes indicative for ammonia-oxidation, was identified in either of the two metagenomes.The complete genome of “Ca. N. islandicus” was uploaded to the MicroScope p […]

library_books

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

2018
Nat Commun
PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] m. Unitig sequences were extracted from GFA files. Canu assemblies were generated using the default parameters and the complete canu pipeline. Three rounds of consensus correction was performed using racon based on minimap overlaps, and the resulting assembly was polished using Illumina PCR-free 2 × 250 bp reads mapped with bwa and pilon. Genome stats were generated using QUAST. The resulting asse […]

library_books

The long reads ahead: de novo genome assembly using the MinION

2017
F1000Res
PMCID: 5770995
PMID: 29375809
DOI: 10.5256/f1000research.12992.r24090

[…] y. The graphical fragment assembly (GFA) output format of Miniasm conveniently allows both graphing of the uncorrected assembly and addition of consensus error correction tools, such as Nanopolish or Racon, to the pipeline.In March of 2016, the authors of Minimap and Miniasm reported assembly of MinION reads of an E. coli genome in a single contig. In May of the same year, Judge et al. assembled a […]

Citations

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Racon institution(s)
Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, Croatia; Centre for Informatics and Computing, Ruder Boskovic Institute, Zagreb, Croatia; Genome Institute of Singapore, Singapore, Singapore; Bioinformatics Institute, Singapore, Singapore

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