Hammer is a tool for error correction of short read datasets with non-uniform coverage, such as single-cell data.
In particular, Hammer does not make any uniformity assumptions on the distribution of the reads along the genome.
It is based on a combination of the Hamming graph build from the set of k-mers and a simple probabilistic model for sequencing errors.
The method is fully described in Medvedev, P., Scott, E., Kakaradov, B., Pevzner, P., Error correction of high-throughput sequencing datasets with non-uniform coverage, Bioinformatics (2011) 27 (13): i137-i141.
Updated version of Hammer (0.2) is out. It fixes several bugs.
First version of Hammer (0.1) is out!
Please contact pmedvedev ]at[ cs ]dot[ ucsd dot edu for any comments/questions.