Subtractive Assembly

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, subtractive 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.

We further developed concurrent subtractive assembly (CoSA), which is an improved version of the subtractive assembly approach for detecting differential reads between two groups of metagenomes. Please check CoSA out at https://sourceforge.net/projects/concurrentsa/.

* This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY