CoSA

CoSA (Concurrent Subtractive assembly) is a package to detect differential short sequencing reads by comparing two groups of metagenomes on the basis of kmer frequencies. KMC 2 is one of the fastest k-mer counting implementations, so we employ KMC 2 for k-mer counting in our package. Because in many cases we need to compare tens of or even hundreds of samples, we adopt the concurrent hash table in Libcuckoo for efficient k-mer counting. Once the differential reads are extracted, they can be used for downstream analysis including assembly to identify genes that are differentially abundant between groups of metagenomes (e.g., healthy vs diseased).

Please refer to our RECOMB paper for more details:
Wontack Han, Mingjie Wang and Yuzhen Ye. A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes. Proceeding of RECOMB 2017.