An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

About

My name is Lex Nederbragt. I am a bioinformatician working at the Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.

I am in charge of the team behind the next-generation sequencing platform at our institute, which is part of the Norwegian High-Throughput Sequencing Centre (NSC). We perform PacBio and 454 sequencing for research groups in Norway and other countries.

My main responsibilities are coordination of the activities and contact with users. I am also chiefly responsible for the bioinformatic analysis of the data.

In our research group, the instrument is used for bacterial de novo sequencing, metagenomics and the sequencing of the cod genome. For these projects, I am performing assemblies and downstream analysis.

You can follow me on twitter, read my other blog, or learn more about me here.

DISCLAIMER: I am not involved in developing newbler, nor am I in any way associated with 454Life Sciences/Roche. I am ‘just’ a frequent user of the program interested in sharing his knowledge.

22 Responses to “About”

  1. Vincent Liu said

    Thank you for your excellent blog.

    What is new in Newbler version 2.5?

    Maybe you know the answer.

    Regards,
    Vincent Liu

  2. Colin said

    Apparently Newbler 2.5 will be available via FTP in “a few weeks”. Some apparently have access already : is was already used in Kumar and Blaxter 2010, BMC Genomics, which appears to show it has some advantages over 2.3.

  3. Rodolfo Aramayo said

    Hi Lex,

    Excellent Blog. I was wandering if you could guide to the place where Newbler can be downloaded?

    Thank You

    Keep Up the Good Work

    –Rodolfo

  4. Gina said

    Excellent blog. It helps me a lot!!

    But I have a doubt? For annotation processes, what is better to use? 454Isotigs.fna or 454AllContigs.fna

    Sorry if I miss this!!

    Thanks, Gina

    • flxlex said

      Thanks! As isotigs should be longer than contigs and less fragmented, I would start with those. Just be careful that there might be redundancy among the isotigs within an isogroup (some can be about the same length and nearly the same sequence).

  5. Ming said

    Thanks for you to develop such a excellent assembler. It works fine for small genome assembly, but it seems to be too much for an big genome, the “Computing alignments” step is very time-consuming, and some times I will got stuck at “Level 1, Phase 8, Round 1…”.
    Would you develop a multi-thread version in any future, at least for those steps?
    Best wishes.

    • Ming said

      Oh, sorry, I got this:
      runAssembly -o project1 -large -cpu 8 /data/sff/EYV886410.sff

      Thank your blog very much !!

    • flxlex said

      First, let me stress that I am not developing newbler! Your comment made me ad this explicitly to the ‘About’ page…

      To answer your question, if you look at this post, you will see that newbler can in fact run in multi-threaded mode, using the -cpu flag. This should significantly speed up your assembly!

  6. Soni said

    Hello Lex,

    Thanks for this wonderful blog. It has helped me understand quite a few concepts for de novo assembly. Would you have much experience with gsMapper? I am struggling to understand the structural variation outputs from it.

    Many thanks

  7. Björn Canbäck said

    Please add a flattr icon so I can contribute. See info at http://flattrchattr.com/2011/06/20/flattr-in-wordpress-com/

  8. I always wondered why Biologists dont share knowledge like computer scientists! Many of my friends who were newbies (computer science) became experts later & became independant by learning from blogs like this! This is really great & thanks for sharing the knowledge!
    Things are changing now!
    raghul

  9. vishal desai said

    Hi Lex Nederbragt, tons of thanks for your wonderful knowledgeble blog. I have used Newbler but didn’t know how its work and also so many other things about Roche 454 assembly. I have little problem related to assembly, once I had use Newbler with my friends helps but that time I got only .fna file not other file like .txt or matrics and etc, so what should I do now I saw your perl scripts. There is no doubt that they are works good but I have .fna so I cant run, please give me advice that what should I do? Thanks in advance. Have graet time ahead.

    • Thanks for your kind words :-)

      You have to get hold of the relevant files in order to be able to use the scripts. Also, I haven’t tested them in a while, so I can’t be sure they still work with the latest versions of newbler…

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