Using pseudoalignment and base quality to accurately quantify microbial community composition
Fig 1
(1) Query reads are pseudoaligned against an index of the reference database, resulting in a set of references they could have potentially originated from. (2) The query reads are locally aligned to the possible references. (3) Using the best alignment, the likelihood that a read originated from a specific reference is calculated. (4) Using the read likelihoods an EM-algorithm is employed to estimate the relative abundances of the references in the pool of query reads.