MuffinEc: Error correction for de Novo assembly via greedy partitioning and sequence alignment.

•We present an error correction method based on grouping reads and Multiple Sequence Alignment (MSA).•This method supports any sequencing technology because it handles all types of errors, including indels.•PacBio datasets can be corrected without an existing genome or a helper dataset with less errors.•Our method is faster and uses less memory than the state of the art.•MuffinEc obtains better sensitivity, specificity and gain in most of our experiments.