songweizhi / MarkerMAG

Linking MAGs with 16S rRNA marker genes
GNU Affero General Public License v3.0
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MarkerMAG: linking MAGs with 16S rRNA marker genes using paired-end short reads

pypi licence pypi version Bioconda DOI

Publication

Updates

MarkerMAG modules

  1. Main module

    • link: linking MAGs with 16S rRNA marker genes
  2. Supplementary modules

    • rename_reads: rename paired reads (manual)
    • matam_16s: assemble 16S rRNA genes with Matam (manual)
    • barrnap_16s: identify 16S rRNA genes from genomes/MAGs with Barrnap (manual)

How to install

How to run

Output files

  1. Summary of identified linkages at genome level:

    Marker MAG Linkage Round
    matam_16S_7 MAG_6 181 Rd1
    matam_16S_12 MAG_9 102 Rd1
    matam_16S_6 MAG_59 55 Rd2
  2. Summary of identified linkages at contig level (with figure):

    Marker___MAG (linkages) Contig Round_1 Round_2
    matam_16S_7___MAG_6(181) Contig_1799 176 0
    matam_16S_7___MAG_6(181) Contig_1044 5 0
    matam_16S_12___MAG_9(102) Contig_840 102 0
    matam_16S_6___MAG_59(39) Contig_171 0 55

    linkages

  3. Copy number of linked 16S rRNA genes.

  4. Visualization of individual linkage.

    MarkerMAG supports the visualization of identified linkages (needs Tablet). Output files for visualization (example) can be found in the [Prefix]_linkage_visualization_rd1/2 folders. You can visualize how the linking reads are aligned to MAG contig and 16S rRNA gene by double-clicking the corresponding ".tablet" file. Fifty Ns are added between the linked MAG contig and 16S rRNA gene.

    linkages

    *If you saw error message from Tablet that says input files format can not be understood, please refer to here for a potential solution.