SPAdes
Genome assembler for single-cell and isolates data sets
Version: see VERSION

Developed in Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University.
Developed in Algorithmic Biology Lab of St. Petersburg Academic University of the Russian Academy of Sciences.

Current SPAdes contributors:

    Dmitry Antipov,
    Anton Bankevich,
    Yuriy Gorshkov,
    Alexey Gurevich,
    Anton Korobeynikov,
    Dmitriy Meleshko,
    Sergey Nurk,
    Andrey Prjibelski,
    Yana Safonova,
    Alla Lapidus and
    Pavel Pevzner

Also contributed:

    Max Alekseyev,
    Mikhail Dvorkin,
    Alexander Kulikov,
    Valery Lesin,
    Sergey Nikolenko,
    Son Pham,
    Alexey Pyshkin,
    Vladislav Saveliev,
    Alexander Sirotkin,
    Yakov Sirotkin,
    Artem Tarasov,
    Glenn Tesler,
    Irina Vasilinetc,
    Nikolay Vyahhi

Installation instructions and manual can be found on the website:
http://bioinf.spbau.ru/spades

References:

Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin,
Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler,
Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021

Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov,
Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin,
Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken,
Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner.
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes
in Computer Science 7821 (2013), pp. 158-170. doi:10.1007/978-3-642-37195-0_13

