Resources

I need one page to collate software and docs I come across, and that is or might be useful to me. Let’s hope this does not become a total mess, and would be useful to others.

Short read assembly:

Nick Loman’s xbase. For short read annotation and assembly. This goes hand in hand with his sage advice page. Also, this document from Illumina

Velvet, of course. De-novo assemblies.

Standardized velvet assembly report from Jeremy Leipzig.

MetaVelvet for metagenomic assemblies.

MIRA for scaffolded assemblies.

 

 

Annotation resources:

RAST & MG-RAST for genomes and metagenomes respectively.

Microbial ecology:

QIIME from Rob Knight’s lab

Mothur from Pat Schloss’s lab.

Share and Enjoy:
  • Fark
  • Digg
  • Technorati
  • del.icio.us
  • StumbleUpon
  • Facebook
  • Reddit
  • Twitter
  • FriendFeed
  • PDF
  • email
  • Print
  • Google Bookmarks

5 Responses to “Resources”

  1. Unum says:

    Hi there! I was doing some Saturday reading on my favorite subject of smORFs and I came across your entry http://bytesizebio.net/index.php/2012/04/27/its-a-smorf-world-after-all/
    I’m a PhD student at the Couso lab at the University of Sussex and I wanted to correct the collaboration. Thanks for highlighting the importance of the small genes we work with. The discovery of the first smORF in Drosophila (tal) was pure chance and we are now well underway with characterising others that have been found as a result of the pipeline in question – and it looks pretty good. Stay tuned for more results! (fingers crossed) 🙂
    Cheers! I really enjoyed browsing your blog.

  2. Marina Thomas says:

    Hello,

    Hope you are doing great.

    My name is Marina, I’m looking for “Business/Funding” related sites and blogs, I recently came across your blog and found it very interesting.

    The article is related to your website and will be appreciated by your readers.

    I guarantee you that the article will be 100% unique, top quality and copy-scape protected and will not be shared with any other site.

    Do let me know so I can send you an article.

    Will be waiting for a reply…

    Thanks,
    Marina

  3. Egle Joseph says:

    Hello,

    I hope you are doing great!

    Recently I came across your website and I found your blog posts very helpful and informative!

    As well, I would like to reccommend adding another great website https://vtex.lt/ which blog I also love to read. I would like to share my thoughts and publish article on your website as well, if interested.

    Thanks in advance for your answer. Please feel free to contact me with any questions you may have.

    Cheers!

  4. Darylpaymn says:

    Mega Darknet – это надежный сервис, где анонимность и конфиденциальность становятся foundation цифровой реальности. Имя “Mega Darknet” is linked с множеством возможностей и интригой. Это не просто веб-сайт; это gateway в hidden world интернета, где регуляции и ограничения lose their power.
    сайт Mega

  5. Humminbirdkli says:

    from lat. manus – “hand” and scribo – “I write”) [1]

Leave a Response

Time limit is exhausted. Please reload the CAPTCHA.