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PBSuite

Free download PBSuite Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named PBSuite whose latest release can be downloaded as PBSuite_15.8.24.tgz. It can be run online in the free hosting provider OnWorks for workstations.

Download and run online this app named PBSuite with OnWorks for free.

Follow these instructions in order to run this app:

- 1. Downloaded this application in your PC.

- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 3. Upload this application in such filemanager.

- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.

- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 6. Download the application, install it and run it.

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PBSuite


DESCRIPTION

This currently hosts two projects created and maintained by Adam English.

PBJelly - the genome upgrading tool.
PBHoney - the structural variation discovery tool

Both are contained within the PBSuite code found in downloads.

----- PBJelly -----
Read The Paper
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

----- PBHoney -----
Read The Paper
http://www.biomedcentral.com/1471-2105/15/180/abstract

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.



Features

  • Genome Assembly
  • Genome Upgrade
  • Structural Variation
  • Assembly Evaluation


Audience

Science/Research



Programming Language

Python


Categories

Bio-Informatics

This is an application that can also be fetched from https://sourceforge.net/projects/pb-jelly/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.


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