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Protocols

Phusion specifications

Information


Unique identifier OMICS_24945
Name Phusion
Alternative name Phusion2
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline James Mullikin

Publication for Phusion

library_books

The Phusion Assembler

2003 Genome Res
PMCID: 430959
PMID: 12529309
DOI: 10.1101/gr.731003

Phusion citations

 (13)
library_books

The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

2018
Cancer Cell
PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] DFT2)) and two host genomes (202H1 and 203H). We used Fermi () to perform base error corrections for raw reads, to remove erroneous sequencing data and to generate a contig-wise assembly. We also ran Phusion2 () to obtain a second assembly with the base error corrected short reads. SOAPdenovo () was used to process the cleaned reads in a third assembly run, which was improved using SSPACE (). Next […]

library_books

Evolutionary Histories of Transposable Elements in the Genome of the Largest Living Marsupial Carnivore, the Tasmanian Devil

2015
Mol Biol Evol
PMCID: 4408412
PMID: 25633377
DOI: 10.1093/molbev/msv017

[…] ze) () and assembled with CABOG (). “WTSI_Devil_ref v7.0” assembly was sequenced by applying Illumina using short insert and mate pair (3,000–10,000 nt insert sizes) libraries, and assembled with the Phusion2 genome assembly pipeline (). Additionally, the WTSI_Devil_ref v7.0 assembly is based on Illumina sequencing of individual chromosomes as well as transcriptomes (). The Cedric assembly consist […]

library_books

Human Infection with Influenza Virus A(H10N8) from Live Poultry Markets, China, 2014

2014
PMCID: 4257803
PMID: 25425075
DOI: 10.3201/eid2012.140911

[…] esized from the viral RNA by reverse transcription PCR by using a SuperScript First-Strand Synthesis System for RT-PCR Kit (Invitrogen, Carlsbad, CA, USA). All gene segments were amplified by using a Phusion High-Fidelity PCR Kit (New England Biolabs, Ipswich, MA, USA). The PCR products were sequenced and the sequences were edited and aligned by using BioEdit software (http://www.mbio.ncsu.edu/bio […]

call_split

Development of Novel Microsatellite Markers for the BBCC Oryza Genome (Poaceae) Using High Throughput Sequencing Technology

2014
PLoS One
PMCID: 3954799
PMID: 24632997
DOI: 10.1371/journal.pone.0091826
call_split See protocol

[…] nd then sequenced using the Illumina Hi Seq 2000 sequencer (Illumina Inc., San Diego, CA, USA). The genome of W303 (European Bioinformatics Institute; Accession number: PRJEB5091) was assembled using Phusion2 and Phrap . The N50 length of the entire assembly was calculated for the initial contigs with small contigs <1000 bp excluded.The SSRs were identified by the software MISA (Microsatellite id […]

library_books

Fatal Metacestode Infection in Bornean Orangutan Caused by Unknown Versteria Species

2014
PMCID: 3884733
PMID: 24377497
DOI: 10.3201/eid2001.131191

[…] e subunit 1 (nad1), published primers JB11 (5′-AGATTCGTAAGGGGCCTAATA- 3′) and JB12 (5′-ACCACTAACTAATTCACTTTC-3′) were used (). PCRs were conducted in 20-μL volumes with 1-μL DNA template by using the Phusion kit (New England Biolabs Inc., Ipswich, MA, USA), cycled as follows: 98°C, 30 s; 35 cycles of 94°C, 10 s, annealing, 30 s, 72°C, 30 s; and final extension at 72°C for 10 min (annealing tempera […]

library_books

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

2012
BMC Biol
PMCID: 3570280
PMID: 23259493
DOI: 10.1186/1741-7007-10-107

[…] We used the Mnemiopsis draft genome, which was previously sequenced using 454 and Ilumina sequencing and assembled into scaffolds [] using the Phusion assembler []. The current draft assembly comprises 5,100 scaffolds (scaffold N-50 of 123 kb), which corresponds to coverage of approximately 12X. A total of 16,645 protein-coding gene models w […]

Citations

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Phusion institution(s)
Informatics Department, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
Phusion funding source(s)
Supported by The Wellcome Trust.

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