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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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k-mer count 估计基因组大小-KmerGenie  

2013-07-16 14:39:20|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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http://kmergenie.bx.psu.edu/

KmerGenie
---------

installation:

    1) Prerequisite: Python >= 2.5 and R.
    2) Type `make` in the KmerGenie directory

    * To enable larger values of k, e.g. 200, type `make k=200`.
    
usage:

    ./kmergenie reads_file

reads_file is either a FASTA, FASTQ, FASTA.gz, FASTQ.gz file or a list of filenames, with one file name per line.

    type ./kmergenie to see extra options

input:

    Input reads should be exactly those the de novo assembler will use to create contigs, i.e. the list of all single and paired-end reads.

    The order does not matter, KmerGenie treats the reads as an unordered set of k-mers. Orientation of the reads also does not matter.
    With Velvet, if you have mate-pairs, Velvet uses them to create contigs, so do include them in KmerGenie.
    Otherwise, if the mate-pairs are used only for scaffolding (i.e. asm_flag=2 in SOAPdenovo), do not include them.

tips:

    By default, KmerGenie will perform another pass to estimate k more precisely. To skip it, specify "--one-pass".
    To run multiple instances of KmerGenie on the same folder, specify the -o and -t parameters (with output prefixes, and less threads per instance).

outputs:

    histograms.dat
        file containing the predicted number of genomic kmers for each k value
    histograms-k*.histo
        files containing approximate histograms for each k value
    histograms-k*.histo.pdf
        plots of the histograms and the fits
    <stdout>
         last line is the best k value

另一软件为:

jellyfish

http://fhqdddddd.blog.163.com/blog/static/18699154201352403249850/

http://www.cbcb.umd.edu/software/jellyfish/

http://www.plob.org/2012/06/06/2055.html
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