Subtractive assembly for comparative metagenomics
- Introduction: Subtractive Assembly is a de novo approach for comparative metagenomics by assembling the differential portion of reads directly. Given two metagenomic datasets A and B, substractive assembly approach first identifies reads that are likely sampled from abundant or unique genomes in A (or B vice versa), using Bloom-filter based k-mer counting. And one can assemble only these reads separately using metagenomic assemblers such as IDBA-UD.
- Download the package from SourceForge
- Get the package with example datasets for using the SAcounter: SAtest.tz (Warning: big file!)
- The subtractive assembly results of the type 2 diabetes (T2D) metagenomes:
- Citation: Mingjie Wang, Thomas G. Doak, and Yuzhen Ye. Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. Genome Biology, 2015 (accepted)
- Contact: Yuzhen Ye (firstname.lastname@example.org) (web)