Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

IDBA-Tran | A de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

Assembles reads to reconstruct expressed transcripts. IDBA-Tran calculates the probability that a k-mer or short simple path contains error by using both their multiplicity and a multi-normal distribution to model the multiplicities of all k-mers in the whole component. The software also aligns reads to the transcript for supplying an estimated expression level for each transcript. It aims to improve accuracy especially for low-expressed transcripts.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

IDBA-Tran forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

IDBA-Tran classification

IDBA-Tran specifications

Unique identifier:
OMICS_01318
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
GCC
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++, Shell (Bash)
Stability:
Stable
Maintained:
Yes

IDBA-Tran distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

download

IDBA-Tran support

Maintainers

  • Francis Chin <>
  • Yu Peng <>

Additional information

The software is also available via Docker.

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Department of Computer Science, The University of Hong Kong, Hong Kong; CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy Sciences, Shanghai, China

Funding source(s)

Supported, in part, by RGC HKU 7111/12E and HKU 719709E, the Shanghai Pujiang Plan (Y057C11501) and Bill & Melinda Gates Foundation Project (‘‘C4 Rice’’).

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.