## SPAdes Genome Assembler changelog

### SPAdes 3.13.0, 11 October 2018

CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected automatically based on read length.

CHANGE: Added manual as README.md in markdown format for github.

FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.

FIX: Assert for path.length() > 0 in rnaSPAdes.

FIX: CQF and k-mer counting.

### SPAdes 3.12.0, 14 May 2018

NEW: Support for merged paired-end reads.

NEW: Experimental pipeline for metagenome hybrid assemblies.

NEW: Standalone graph builder application.

NEW: Standalone k-mer counting application.

NEW: Standalone long read to graph aligner.

CHANGE: Significant improvements in hybrid assembly pipeline.

CHANGE: Faster read alignment using BWA.

CHANGE: Improvements in metaSPAdes results.

CHANGE: More sensitive results for rnaSPAdes.

CHANGE: All binaries for SPAdes pipeline steps now have `spades-` prefix in its name.

CHANGE: Better running time and RAM consumption for graph construction stage.

CHANGE: Overall performance improvements.

FIX: K value estimation for rnaSPAdes.

DEPRECATED: dipSPAdes pipeline for highly polymorphic diploid genomes (still present in the release but no longer supported).

### SPAdes 3.11.1, 1 October 2017

FIX: Handling spaces in path during mismatch correction.

FIX: Python3 support in rnaSPAdes.

FIX: K value estimation for long reads.

FIX: Processing long reads alignments.

### SPAdes 3.11.0, 1 September 2017

NEW: Support for strand-specific RNA-Seq data in rnaSPAdes.

NEW: Coverage based isoform detection in rnaSPAdes.

NEW: Reworked IonHammer read error correction module.

CHANGE: Improved tandem repeat resolution accuracy.

CHANGE: Better performance of exSPAnder module.

CHANGE: metaSPAdes pipeline improvements.

CHANGE: Better running time and RAM consumption for the entire pipeline.

FIX: Incomplete paths in GFA output.

FIX: Mismatch and indel rate in careful mode for isolate datasets (esp. low covered ones).

FIX: Occasional hanging of edge disconnection procedure in metaSPAdes.

### SPAdes 3.10.1, 1 March 2017

FIX: Build for MacOS.

FIX: Minor bugs in hybridSPAdes pipeline.

FIX: `--continue` option for metaSPAdes.

FIX: `--tmp-dir` is now works correctly for MismatchCorrector.

FIX: `Assertion `overlap <= k_' failed` in rnaSPAdes and metaSPAdes.

FIX: `Assertion `path.Length() > 0' failed` in metaSPAdes.

### SPAdes 3.10.0, 27 January 2017

NEW: Scaffolding algorithm for mate-pairs and long reads.

NEW: Contigs and graph output in GFA format.

CHANGE: Better running time and RAM consumption for all pipelines.

CHANGE: Improvements in metagenomic pipeline.

CHANGE: Improved isoform detection algorithm in rnaSPAdes.

### SPAdes 3.9.1, 4 December 2016

FIX: macOS Sierra crash.

### SPAdes 3.9.0, 23 July 2016

NEW: rnaSPAdes pipeline for de novo transcriptome assembly from RNA-Seq data.

CHANGE: Improved memory consumption in metagenomic pipeline.

FIX: Several minor bugs.

### SPAdes 3.8.2, 10 July 2016

FIX: Several minor bug-fixes for metaSPAdes and SPAdes pipelines.

### SPAdes 3.8.1, 8 June 2016

FIX: plasmidSPAdes now works with PacBio/Nanopore reads.

### SPAdes 3.8.0, 1 June 2016

NEW: Added plasmidSPAdes – a pipeline designed for extracting and assembling plasmids from WGS data sets.

CHANGE: Significant improvements in metaSPAdes performance.

CHANGE: Improved running time and RAM consumption.

### SPAdes 3.7.1, 8 March 2016

FIX: MismatchCorrector fixed for MaxOS.

### SPAdes 3.7.0, 24 February 2016

NEW: metaSPAdes metagenomic pipeline.

CHANGE: improved performance for both error correction and assembly stages.

FIX: Multiple bug fixes.

### SPAdes 3.6.2, 20 November 2015

NEW: Contigs/scaffolds paths for assembly_graph.fastg in Bandage-supported format.

FIX: Multithreaded MismatchCorrector.

FIX: BayesHammer bug fixes.

FIX: Python 3.5 support; python 3 support for truSPAdes.

### 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.

SPAdes website