MBMC a novel taxonomy-dependent and alignment-free metagenomic reads binning approach in metagenomic studies. Different from all existing methods, MBMC bins reads by measuring the similarity of reads to the learned 9-th order Markov models for different taxa, instead of directly comparing reads with known genomic sequences.

Download

Download the Software and manual.

Inputs

There are only three parameters for MBMC.
  1. Reads files (Required): paired-end or single-end reads in FASTA format
    Paired-end reads should be in following format:
    >Read1_end1
    ACGT...
    >Read1_end2
    ACGT...
    >Read2_end1
    ACGT...
    >Read2_end2
    ACGT...

  2. Cutoff c (Optional): the cutoff to determine the number of species, by default c=0.05.
    This cutoff means that the binned group of reads which account for more than c of total reads will be regarded as a predicted species.

  3. Read type: 0 or 1 (Optional), by default Read type=0;
    0: denotes paired-end reads;
    1: denotes single-end reads;

Outputs

MBMC provided us the detailed running process and binned reads.
  1. MBMC running process, which are shown in the output window.
  2. MBMC binned read files: input reads are binned into separate files in FASTA format, which can be found in the folder "ReadsFileName_binned".
See manual for the details of how to use MBMC.

For any questions, please contact us with emails:
  • Ying Wang: ying2010@knights.ucf.edu
  • Haiyan Hu: haihu@cs.ucf.edu
  • Xiaoman Li: xiaoman@mail.ucf.edu