SPAdes Genome Assembler changelog

SPAdes 3.6.1, 4 October 2015

CHANGE: No misleading FASTG files, only assembly graph is saved in FASTG format.

FIX: Multiple bugfixes.

SPAdes 3.6.0, 17 August 2015

NEW: Added truSPAdes – an assembler for short reads produced by Illumina TruSeq Long Read technology.

CHANGE: Better running time, less RAM consumption and improved results for BayesHammer error correction module.

CHANGE: Improvements and bugfixes in repeat resolution and scaffolding modules.

CHANGE: Improvements and bugfixes in dipSPAdes.

CHANGE: MismatchCorrector now uses bwa-mem.

FIX: Bugfixes in MismatchCorrector.

SPAdes 3.5.0, 7 December 2014

NEW: New MismatchCorrector module.

NEW: Support for Oxford Nanopore long reads.

NEW: Support for Lucigen NxMate mate-pair libraries.

NEW: Possibility to specify coverage cutoff: automatic and manual.

CHANGE: Better running time.

CHANGE: Improved RAM consumption.

CHANGE: High-quality mate-pairs are now assumed to have forward-revers orientation (same as paired-end).

FIX: Fixed FASTG format.

SPAdes 3.1.1, 27 May 2014

FIX: Several improvements in IonHammer.

FIX: Fixed a few minor bugs in repeat resolution and scaffolding.

SPAdes 3.1.0, 27 May 2014

NEW: Mate-pair only assembly with high-quality libraties.

NEW: Support for BAM files.

CHANGE: Improved IonTorrent pipeline.

CHANGE: Better quality and higher performance when using mate-pairs.

FIX: Fixed dipSPAdes bugs and user interface.

SPAdes 3.0.0, 29 December 2013

NEW: Module for assemblying diplod highly polymorphic genomes.

NEW: Support for PacBio reads.

NEW: Support for IonTorrent reads.

NEW: Support for Sanger reads and additional contigs.

NEW: Possibility to restart SPAdes starting from the specified check-point with the --restart-from option.

NEW: Output contigs/scaffolds in FASTA and FASTG.

CHANGE: Improved algorithm for mate-pair repeat resolution and scaffolding.

CHANGE: Improved N50 and misassembly rate for single-cell data sets with low genome fraction.

FIX: User-friendly handling for errors in mismatch corrector.

REMOVE: Rectangle graph repeat resolution module.

SPAdes 2.5.1, 10 September 2013

NEW: Python 3.2 and 3.3 compatibility.

NEW: Possibility to continue SPAdes run starting from the last check-point with the --continue option.

CHANGE: Decreased memory consumption for error correction module.

CHANGE: Improved misassembly rate for single-cell data sets with low genome fraction.

FIX: User-friendly handling for the case when paired reads do not align to the assembly graph.

SPAdes 2.5.0, 2 July 2013

NEW: Multiple paired-end and mate-pair libraries.

NEW: Recipe for assembling Illumina 2x150bp and 2x250bp reads.

CHANGE: Improved mismatch and indel rate.

SPAdes 2.4.0, 26 February 2013

NEW: Mismatch correction post-processing module.

NEW: Rectangle graph repeat resolution module as an option.

NEW: Build for Mac OS.

CHANGE: Improved assembly quality of standard (isolate) data sets.

CHANGE: Decreased memory consumption in error correction module (14 Gb instead of 24 Gb on E.coli test dataset).

REMOVE: SAM-file generation.

SPAdes 2.3.0, 30 October 2012

NEW: Generate scaffolds alongside with contigs.

CHANGE: Use N instead of A, C, G, T for the variations in repeats.

CHANGE: Memory requirements for E.coli test dataset decreased from 35 Gb to 24 Gb of RAM.

CHANGE: output_dir is a required command line parameter instead of project_name.

CHANGE: Simplified output directory structure.

CHANGE: CMake 2.8 is required instead of 2.6.

REMOVE: No dependency from boost library.

SPAdes 2.2.1, 20 August 2012

FIX: Avoid Verification of expression 'v1 == conjugate(v2)' failed error.

SPAdes 2.2.0, 2 August 2012

NEW: No special binaries for different K values.

NEW: Great improvements in error correction tool BayesHammer.

CHANGE: Memory requirements for E.coli test dataset decreased from 85 Gb to 35 Gb of RAM.

CHANGE: Only 1 iteration of BayesHammer by default.

NEW: Improved assembly quality.

SPAdes 2.1.0, 28 May 2012

NEW: Support multi-threading.

NEW: Improved algorithms.

NEW: Command-line interface.

CHANGE: Quality assesment separated from the core pipeline.

REMOVE: No support for debian and RPM packages.

SPAdes 2.0.1, 26 Apr 2012

FIX: Quality tool fixed.

SPAdes 2.0.0, 18 Apr 2012

Initial release.

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