Tag: atlas

ATLAS 2.6a2 – Analyzing your Metagenome data

ATLAS 2.6a2

:: DESCRIPTION

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ATLAS

:: MORE INFORMATION

Citation

Kieser S, Brown J, Zdobnov EM, Trajkovski M, McCue LA.
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
BMC Bioinformatics. 2020 Jun 22;21(1):257. doi: 10.1186/s12859-020-03585-4. PMID: 32571209; PMCID: PMC7310028.

Atlas 2005 – Whole Genome Assembly Suite

Atlas 2005

:: DESCRIPTION

Atlas is a collection of software tools to facilitate the assembly of large genomes from whole genome shotgun reads, or a combination of whole genome shotgun reads and BAC or other localized reads.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Atlas

:: MORE INFORMATION

Pathway Projector – Zoomable Pathway Browser using KEGG Atlas

Pathway Projector

:: DESCRIPTION

The Pathway Projector was implemented according to the aforementioned requirements, including the availability of a large-scale comprehensive pathway map, pathways from a wide variety of organisms, and searching and mapping capabilities.

::DEVELOPER

PathwayProjector team

:: SCREENSHOTS

Pathwayprojector

:: REQUIREMENTS

  • Web Browser 
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M.
PLoS One. 2009 Nov 11;4(11):e7710. doi: 10.1371/journal.pone.0007710.

CellExplorer 1.0 – 3D C. elegans atlas Building & Application Tools

CellExplorer 1.0

:: DESCRIPTION

CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.

::DEVELOPER

Peng Lab @ JANELIA of HHMI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

CellExplorer

:: MORE INFORMATION

Citation:

Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, and Eugene Myers,
“A 3D digital atlas of C. elegans and its application to single-cell analyses,”
Nature Methods, doi:10.1038/nmeth.1366, 2009.

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