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spades (version 1.0)

Single-cell?:

This option is required for MDA (single-cell) data.

Run only assembly? (without read error correction):

Careful correction?:

Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes).

K-mers to use, separated by commas:

Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55.

Coverage Cutoff:

Libraries are IonTorrent reads?:

Library

Libraries 0

PacBio CLR reads

PacBio CLR reads 0

Nanopore reads

Nanopore reads 0

Sanger reads

Sanger reads 0

Trusted contigs

Trusted contigs 0

Untrusted contigs

Untrusted contigs 0

What it does

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.

This wrapper runs SPAdes 3.5.0, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.

SPAdes citation

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. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021.

License

SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.

This wrapper is copyrighted by Lionel Guy,Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

** Acknowledgments **

Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.

Nicola Soranzo fixed various bugs.