MakeHub 1.0.5 – Fully Automated Generation of UCSC Assembly Hubs

MakeHub 1.0.5

:: DESCRIPTION

MakeHub is a command line tool for the fully automatic generation of of track data hubs for visualizing genomes with the UCSC genome browser. Track data hubs are data structures that contain all required information about a genome for visualizing with the UCSC genome browser.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

MakeHub

:: MORE INFORMATION

Citation

Hoff KJ.
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs.
Genomics Proteomics Bioinformatics. 2019 Oct;17(5):546-549. doi: 10.1016/j.gpb.2019.05.003. Epub 2020 Jan 28. PMID: 32001327; PMCID: PMC7056914.

Ruby UCSC API 0.6.5 – An API for the UCSC Genome Database

Ruby UCSC API 0.6.5

:: DESCRIPTION

Ruby UCSC API, a library to access the UCSC genome database using Ruby.It will facilitate biologists to query the UCSC genome database programmatically.

::DEVELOPER

Mishima, Hiroyuki (hmishima at nagasaki-u.ac.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Ruby

:: DOWNLOAD

  Ruby UCSC API

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 21;13:240. doi: 10.1186/1471-2105-13-240.
The Ruby UCSC API: accessing the UCSC genome database using Ruby.
Mishima H, Aerts J, Katayama T, Bonnal RJ, Yoshiura K.

Tbl2KnownGene – Convert NCBI.tbl to UCSC knownGene.txt data file

Tbl2KnownGene

:: DESCRIPTION

Tbl2KnownGene is a wrapper tool that parses the contents of a NCBI .tbl annotation table and produces a UCSC Known Genes annotation table.

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Tbl2KnownGene

:: MORE INFORMATION

Citation

Bioinformation. 2014 Aug 30;10(8):544-7. doi: 10.6026/97320630010544. eCollection 2014.
Tbl2KnownGene: A command-line program to convert NCBI.tbl to UCSC knownGene.txt data file.
Bai Y