Artemis pipeline

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

Taxon


  • Eubacteria

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Tim Carver <>

Additional information


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

Publication for Artemis

Artemis citations

 (4)
2017
PMCID: 5496865

[…] reads. fragments sorted in sam files were counted by htseq count31 for stranded library with the union mode and differential expression calculated using deseq32. bam files were visualized using the artemis browser34., we used the detr’prok27 workflow of 43 steps to identify novel rnas in s. aureus newman. briefly, the pipeline clustered overlapping rna-seq reads from bwa alignments to identify […]

2017
PMCID: 5268413

[…] 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: 5114424

[…] the generated alignment files were manipulated with samtools (59) and a custom script to identify reads with barcodes (gcctcgcga) (57). total and bar-coded reads were then quantified using the artemis genome browser (60). hit-lists generated from rit-seq analyses excluded selected large gene families, including variant surface glycoproteins, and genes immediately adjacent to hits., pcr […]

2015
PMCID: 4415905

[…] 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 […]

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.