丁丁博客

序列拼接软件velvet 1.1.01发布

2011-3-29日发布了velvet最新版本1.1.01，在这一版本中终于支持多线程运行了！！
速度可以提高4-10倍，还有一些另外的修改，附上作者的原话：

Dear Velvet users,

it is my pleasure to announce the release of Velvet 1.1.01!

Sylvain Forêt from ANU did a excellent job multithreading Velvet, 
meaning that it can use multiple CPUs on the same computer, thus freeing 
up the computer that much faster. 4 to 10 fold accelerations have been 
reported. He also reduced the memory footprint, and improved the use of 
mate-pairs, filtering out paired-end contamination.

Also in this new version Yasubumi Sakakibara and colleagues shared their 
MetaVelvet code, which is designed to analyze metagenomic data.

Regards,

Daniel

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Comments

10 responses to “序列拼接软件velvet 1.1.01发布”

  1. 丁丁 Avatar
    丁丁

    今天作者又发布了1.1.02了，修改了一些1.1.01中的错误，更新了Manual

  2. xenophobe Avatar
    xenophobe

    问一下：velvet有没有带注释的代码？

    1. 丁丁 Avatar
      丁丁

      @xenophobe:没有研究过它的源码~

  3. 丁丁 Avatar
    丁丁

    velvet 1.1.04发布，作者声明：
    ”Velvet 1.1.04 is now available on github or
    http://www.ebi.ac.uk/~zerbino/velvet/velvet_latest.tgz. In it:

    – Matthias Haimel found a potentially serious bug which would affect
    paired-read assemblies since v. 1.1.01 (released March 30) – you might
    want to double check your latest assemblies.

    – Sylvain For?t found a bug in the output of gaps within long node sequences
    – A typo was corrected in the Manual
    – As pointed out by several users, the correct coverage of nodes is now
    output in the contigs.fa file
    – Compilation warnings for k < 32 were corrected
    – Adrian Platts suggested that velveth no longer squashes the Log file,
    – Adrian Platts suggested that TourBus display how many nodes are to be
    visited

    Best regards,

    Daniel
    “

  4. RobertoRun Avatar
    RobertoRun

    但是我没找到设置线程的参数啊，楼主的指导麻烦告知一下！

    1. 丁丁 Avatar
      丁丁

      @RobertoRun 根据Manual上的说法在编译的时候用make ’OPENMP=1’的参数就可以了

  5. RobertoRun Avatar
    RobertoRun

    谢谢楼主，找到了！我只看到了下README

  6. 丁丁 Avatar
    丁丁

    Velvet 1.1.22 is now available on github or
    http://www.ebi.ac.uk/~zerbino/velvet/velvet_latest.tgz.

    In it a number of minor modifications:
    – Compilation options are now printed in the Log file
    – A timersub macro was added for Solaris users. (thanks to Nathan Weeks
    for this patch)
    – The Makefile was made POSIX compliant (thanks again to Nathan for this
    patch)
    – The OpenMP compilation flag was standardized to _OPENMP (thanks to
    Nathan for pointing this out)
    – An offset bug was found in Columbus (thanks to Rodolfo Aramayo for
    spotting this)

    Regards,

    Daniel

  7. wufawfua Avatar
    wufawfua

    请问一下：有没有什么工具可以结合已知的基因组序列作为参考来对转录组数据进行拼接啊？？

    1. 丁丁 Avatar
      丁丁

      @wufawfua velvet有columbus扩展可以进行有reference的拼接，另外有Oases扩展可以进行转录组的拼接，你可以试试把这两者结合起来使用~

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