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SPADES: SAINT-PETERSBURG GENOME ASSEMBLER
Copyright (c) 2015-2018 Saint Petersburg State University
Copyright (c) 2011-2014 Saint Petersburg Academic University
SPAdes is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License, Version 2,
dated June 1991, as published by the Free Software Foundation.
SPAdes 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, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-------------------------------------------------------------------------------
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,
Elena Bushmanova,
Vasisliy Ershov,
Yuriy Gorshkov,
Alexey Gurevich,
Anton Korobeynikov,
Sergey Nurk,
Andrey Prjibelski,
Ivan Tolstoganov,
Alla Lapidus and
Pavel Pevzner
Also contributed:
Max Alekseyev,
Mikhail Dvorkin,
Alexander Kulikov,
Valery Lesin,
Dmitriy Meleshko,
Sergey Nikolenko,
Son Pham,
Alexey Pyshkin,
Yana Safonova,
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://cab.spbu.ru/software/spades/
Address for communication: spades.support@cab.spbu.ru
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
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3.13.0-dev
<title>SPAdes Genome Assembler changelog</title>
<body>
<h2>SPAdes Genome Assembler changelog</h2>
<h3>SPAdes 3.13.0, 11 October 2018</h3>
<p>CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected automatically based on read length.</p>
<p>CHANGE: Added manual as README.md in markdown format for github.</p>
<p>FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.</p>
<p>FIX: Assert for path.length() > 0 in rnaSPAdes. </p>
<p>FIX: CQF and k-mer counting. </p>
<h3>SPAdes 3.12.0, 14 May 2018</h3>
<p>NEW: Support for merged paired-end reads.</p>
<p>NEW: Experimental pipeline for metagenome hybrid assemblies.</p>
<p>NEW: Standalone graph builder application.</p>
<p>NEW: Standalone k-mer counting application.</p>
<p>NEW: Standalone long read to graph aligner.</p>
<p>CHANGE: Significant improvements in hybrid assembly pipeline.</p>
<p>CHANGE: Faster read alignment using BWA.</p>
<p>CHANGE: Improvements in metaSPAdes results.</p>
<p>CHANGE: More sensitive results for rnaSPAdes.</p>
<p>CHANGE: All binaries for SPAdes pipeline steps now have <code>spades-</code> prefix in its name.</p>
<p>CHANGE: Better running time and RAM consumption for graph construction stage.</p>
<p>CHANGE: Overall performance improvements.</p>
<p>FIX: K value estimation for rnaSPAdes.</p>
<p>DEPRECATED: dipSPAdes pipeline for highly polymorphic diploid genomes (still present in the release but no longer supported).</p>
<h3>SPAdes 3.11.1, 1 October 2017</h3>
<p>FIX: Handling spaces in path during mismatch correction.</p>
<p>FIX: Python3 support in rnaSPAdes.</p>
<p>FIX: K value estimation for long reads.</p>
<p>FIX: Processing long reads alignments.</p>
<h3>SPAdes 3.11.0, 1 September 2017</h3>
<p>NEW: Support for strand-specific RNA-Seq data in rnaSPAdes.</p>
<p>NEW: Coverage based isoform detection in rnaSPAdes.</p>
<p>NEW: Reworked IonHammer read error correction module.</p>
<p>CHANGE: Improved tandem repeat resolution accuracy.</p>
<p>CHANGE: Better performance of exSPAnder module.</p>
<p>CHANGE: metaSPAdes pipeline improvements.</p>
<p>CHANGE: Better running time and RAM consumption for the entire pipeline.</p>
<p>FIX: Incomplete paths in GFA output.</p>
<p>FIX: Mismatch and indel rate in careful mode for isolate datasets (esp. low covered ones).</p>
<p>FIX: Occasional hanging of edge disconnection procedure in metaSPAdes.</p>
<h3>SPAdes 3.10.1, 1 March 2017</h3>
<p>FIX: Build for MacOS.</p>
<p>FIX: Minor bugs in hybridSPAdes pipeline.</p>
<p>FIX: <code>--continue</code> option for metaSPAdes.</p>
<p>FIX: <code>--tmp-dir</code> is now works correctly for MismatchCorrector.</p>
<p>FIX: <code>Assertion `overlap <= k_' failed</code> in rnaSPAdes and metaSPAdes.</p>
<p>FIX: <code>Assertion `path.Length() > 0' failed</code> in metaSPAdes.</p>
<h3>SPAdes 3.10.0, 27 January 2017</h3>
<p>NEW: Scaffolding algorithm for mate-pairs and long reads.</p>
<p>NEW: Contigs and graph output in GFA format.
<p>CHANGE: Better running time and RAM consumption for all pipelines.</p>
<p>CHANGE: Improvements in metagenomic pipeline.</p>
<p>CHANGE: Improved isoform detection algorithm in rnaSPAdes.</p>
<h3>SPAdes 3.9.1, 4 December 2016</h3>
<p>FIX: macOS Sierra crash.</p>
<h3>SPAdes 3.9.0, 23 July 2016</h3>
<p>NEW: rnaSPAdes pipeline for de novo transcriptome assembly from RNA-Seq data.</p>
<p>CHANGE: Improved memory consumption in metagenomic pipeline.</p>
<p>FIX: Several minor bugs.</p>
<h3>SPAdes 3.8.2, 10 July 2016</h3>
<p> FIX: Several minor bug-fixes for metaSPAdes and SPAdes pipelines.</p>
<h3>SPAdes 3.8.1, 8 June 2016</h3>
<p>FIX: plasmidSPAdes now works with PacBio/Nanopore reads.</p>
<h3>SPAdes 3.8.0, 1 June 2016</h3>
<p>NEW: Added plasmidSPAdes &ndash; a pipeline designed for extracting and assembling plasmids from WGS data sets.</p>
<p>CHANGE: Significant improvements in metaSPAdes performance.</p>
<p>CHANGE: Improved running time and RAM consumption.</p>
<h3>SPAdes 3.7.1, 8 March 2016</h3>
<p>FIX: MismatchCorrector fixed for MaxOS.</p>
<h3>SPAdes 3.7.0, 24 February 2016</h3>
<p>NEW: metaSPAdes metagenomic pipeline.</p>
<p>CHANGE: improved performance for both error correction and assembly stages.</p>
<p>FIX: Multiple bug fixes.</p>
<h3>SPAdes 3.6.2, 20 November 2015</h3>
<p>NEW: Contigs/scaffolds paths for assembly_graph.fastg in Bandage-supported format.</p>
<p>FIX: Multithreaded MismatchCorrector.</p>
<p>FIX: BayesHammer bug fixes.</p>
<p>FIX: Python 3.5 support; python 3 support for truSPAdes.</p>
<h3>SPAdes 3.6.1, 4 October 2015</h3>
<p>CHANGE: No misleading FASTG files, only assembly graph is saved in FASTG format.
<p>FIX: Multiple bugfixes.</p>
<h3>SPAdes 3.6.0, 17 August 2015</h3>
<p>NEW: Added truSPAdes &ndash; an assembler for short reads produced by Illumina TruSeq Long Read technology.</p>
<p>CHANGE: Better running time, less RAM consumption and improved results for BayesHammer error correction module.</p>
<p>CHANGE: Improvements and bugfixes in repeat resolution and scaffolding modules.</p>
<p>CHANGE: Improvements and bugfixes in dipSPAdes.</p>
<p>CHANGE: MismatchCorrector now uses bwa-mem.</p>
<p>FIX: Bugfixes in MismatchCorrector.</p>
<h3>SPAdes 3.5.0, 7 December 2014</h3>
<p>NEW: New MismatchCorrector module.</p>
<p>NEW: Support for Oxford Nanopore long reads.</p>
<p>NEW: Support for Lucigen NxMate mate-pair libraries.</p>
<p>NEW: Possibility to specify coverage cutoff: automatic and manual.</p>
<p>CHANGE: Better running time.</p>
<p>CHANGE: Improved RAM consumption.</p>
<p>CHANGE: High-quality mate-pairs are now assumed to have forward-revers orientation (same as paired-end).</p>
<p>FIX: Fixed FASTG format.</p>
<h3>SPAdes 3.1.1, 27 May 2014</h3>
<p>FIX: Several improvements in IonHammer.</p>
<p>FIX: Fixed a few minor bugs in repeat resolution and scaffolding.</p>
<h3>SPAdes 3.1.0, 27 May 2014</h3>
<p>NEW: Mate-pair only assembly with high-quality libraties.</p>
<p>NEW: Support for BAM files.</p>
<p>CHANGE: Improved IonTorrent pipeline.</p>
<p>CHANGE: Better quality and higher performance when using mate-pairs.</p>
<p>FIX: Fixed dipSPAdes bugs and user interface.</p>
<h3>SPAdes 3.0.0, 29 December 2013</h3>
<p>NEW: Module for assemblying diplod highly polymorphic genomes.</p>
<p>NEW: Support for PacBio reads.</p>
<p>NEW: Support for IonTorrent reads.</p>
<p>NEW: Support for Sanger reads and additional contigs.</p>
<p>NEW: Possibility to restart SPAdes starting from the specified check-point with the <code>--restart-from</code> option.</p>
<p>NEW: Output contigs/scaffolds in FASTA and FASTG.</p>
<p>CHANGE: Improved algorithm for mate-pair repeat resolution and scaffolding.</p>
<p>CHANGE: Improved N50 and misassembly rate for single-cell data sets with low genome fraction.</p>