1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

16. Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar options to filtere out or narrow down your search result. This webpage can be an useful resource for a beginners bioinformatician as it contain several bioinformatics basics script that are commonly used by biological programmers and biologist.

Stand on the slumped, dandruff-covered shoulders of millions of computer nerds. _/\_

Enjoy the code and research work.

http://code.ohloh.net/search?s=bioinformatics

Address of the bookmark: http://code.ohloh.net/search?s=bioinformatics

Qualifications:
MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.

Deadline
01.08.2015

Ruby is a dynamic, reflective, general purpose object-oriented programming language that combines syntax inspired by Perl with Smalltalk-like features. Ruby originated in Japan during the mid-1990s and was initially developed and designed by Yukihiro "Matz" Matsumoto. It was influenced primarily by Perl, Smalltalk, Eiffel, and Lisp.

Ruby supports multiple programming paradigms, including functional, object oriented, imperative and reflective. It also has a dynamic typesystem and automatic memory management; it is therefore similar in varying respects to Python, Perl, Lisp, Dylan, Pike, and CLU.

The standard 1.8.7 implementation is written in C, as a single-pass interpreted language. There is currently no specification of the Ruby language, so the original implementation is considered to be the de facto reference. As of 2010, there are a number of complete or upcoming alternative implementations of the Ruby language, including YARV, JRuby, Rubinius, IronRuby, MacRuby and HotRuby, each of which takes a different approach, with IronRuby, JRuby and MacRuby providing just-in-time compilation and MacRuby also providing ahead-of-time compilation. The official 1.9 branch uses YARV, as will 2.0 (development), and will eventually supersede the slower Ruby MRI.

Ruby Quick Reference
http://www.zenspider.com/Languages/Ruby/QuickRef.html

Ruby Annotation
http://www.w3.org/TR/ruby/

Ruby in Linux Journals
http://www.linuxjournal.com/article/5915

Ruby Documentation: Programming Ruby
http://ruby-doc.org/docs/ProgrammingRuby/

The Top 10 Reasons The Ruby Programming Language Sucks

http://www.slideshare.net/vishnu/the-top-10-reasons-the-ruby-programming-language-sucks

Ruby : The Programmers best friends
http://www.ruby-lang.org/en/

For Ruby Beginners
http://www.squidoo.com/ruby-programming-beginner

Ruby Programming
http://en.wikibooks.org/wiki/Ruby_Programming

Ruby CookBook
http://en.wikibooks.org/wiki/Cookbook:Table_of_Contents

Ruby Programming Challenge for Newbies -
http://rubylearning.com/blog/ruby-programming-challenge-faq/

Common "issues" faced by Ruby Newbies by Chris Strom -
http://japhr.blogspot.com/2009/10/newbie-feedback.html

Books
http://www.sapphiresteel.com/The-Book-Of-Ruby

Free Online Ruby Programming along with many Ruby newbies here -
http://rubylearning.org/class/

More at https://www.raku.org/

Address of the bookmark: https://www.raku.org/

Features

• An amazing real-time web framework, allowing you to easily grow single file prototypes into well-structured MVC web applications.
  • Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/PSGI detection, first class Unicode support and much more for you to discover.
• A powerful web development toolkit, that you can use for all kinds of applications, independently of the web framework.
  • Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.
  • Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.
  • JSON and HTML/XML parser with CSS selector support.
• Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)
• Fresh code based upon years of experience developing Catalyst, free and open source.
• Hundreds of 3rd party extensions and high quality spin-off projects like the Minion job queue.

http://mojolicious.org/

Address of the bookmark: http://mojolicious.org/

The primary home page for DendroPy, with detailed tutorials and documentation, is at:

http://dendropy.org/

DendroPy is also hosted in the official Python repository:

http://packages.python.org/DendroPy/

Address of the bookmark: https://pypi.org/project/DendroPy/

The easiest way to install Gooey is via pip

pip install Gooey 

Alternatively, you can install Gooey by cloning the project to your local directory

git clone https://github.com/chriskiehl/Gooey.git

run setup.py

python setup.py install

Address of the bookmark: https://github.com/chriskiehl/Gooey

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.