Artemis protocols

Artemis specifications

Information


Unique identifier OMICS_00903
Name Artemis
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Javascript, Shell (Bash)
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Medium
Version 17.0.1
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Tim Carver <>

Additional information


http://sanger-pathogens.github.io/Artemis/

Publication for Artemis

Artemis IN pipelines

 (10)
2017
PMCID: 5268413
PMID: 28125655
DOI: 10.1371/journal.pone.0170676

[…] pseudotuberculosis isolated over 16 years (1996–2012)., the nucleotide sequences of ris for the seven sequenced genomes and other five genomes of bacteria isolated in california were recovered with artemis software and analyzed using fragmented all-against-all comparison with the gegenees software v. 2.2.1 [32]. the comparative results of gegenees are presented as a heatmap containing […]

2016
PMCID: 4963484
PMID: 27280420
DOI: 10.1128/JCM.00432-16

[…] same mapping reference. this excluded variants in mobile genetic elements, which were identified by comparing reference genomes with the artemis comparison tool (act) (52) and manually curated using artemis (53). this criterion ensured that isolates were not assigned the same type due to large amounts of missing data. isolates considered nontypeable were still analyzed for the purpose […]

2016
PMCID: 5070307
PMID: 27756224
DOI: 10.1186/s12864-016-3154-8

[…] --no-discordant. approximately 25 million bloodstream-form and 50 million insect stage reads were aligned for each clone. alignment files were manipulated using samtools [51], and visualized in the artemis genome browser [52]. single base resolution plots were generated using the pysam api (https://github.com/pysam-developers/pysam) in an in-house script that filters reads based on alignment […]

2015
PMCID: 4415905
PMID: 25769787
DOI: 10.1016/j.ijantimicag.2015.01.009

[…] the ef-g) to detect mutations conferring resistance towards fusidic acid. staphylococcal cassette chromosome (scc) regions were visualised (including sequence coverage and snp variations) using artemis [14] and were compared using the artemis comparison tool. the fusc-encoding region in the st8 isolate (mrsa18) was highly fragmented and was not analysed further. maximum likelihood […]

2015
PMCID: 4491227
PMID: 26141822
DOI: 10.1186/s12864-015-1661-7

[…] genome (nc002163) using bowtie v2 on the biolinux platform [15, 16]. approximately 97 % of reads aligned for each sequencing run (additional file 1: table s1). aligned reads were visualized using artemis with the bamview plugin [17]. raw read counts for each gene were tabulated (additional file 2: table s2) using bedtools and also used to calculate a reads per kilobase coding sequence per […]

Artemis institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
Artemis funding source(s)
Supported by the Wellcome Trust through their funding of the Pathogen Genomics group at the Wellcome Trust Sanger Institute (grant number WT 076964).

Artemis review

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Pablo Smircich

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Desktop
The Artemis genome browser is also a feature rich annotation tool. I use it frequently when I need to view my own tracks, either annotation or quantitative information.
One of the best and I think a little bit hidden feature is that you can create a configuration file with many options to change the default UI when the software initiates.