From 8456deb2335f1d2e03a25d51b41ee92ddb5b3bac Mon Sep 17 00:00:00 2001 From: Andrey Prjibelski Date: Tue, 14 May 2024 17:35:55 +0300 Subject: [PATCH] convert changelog to markdown --- changelog.html | 439 ---------------------------------------------- changelog.md | 468 +++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 468 insertions(+), 439 deletions(-) delete mode 100644 changelog.html create mode 100644 changelog.md diff --git a/changelog.html b/changelog.html deleted file mode 100644 index 0cfa6b0e0c..0000000000 --- a/changelog.html +++ /dev/null @@ -1,439 +0,0 @@ -SPAdes Genome Assembler changelog - - -

SPAdes Genome Assembler changelog

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SPAdes 3.15.4, 1 February 2022

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FIX: MacOS Monterey memory limit failure.

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FIX: upgrade pyyaml to run correctly with Python 3.10.

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FIX: WSL for py2 check.

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FIX: A few stability fixes.

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SPAdes 3.15.3, 22 July 2021

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FIX: trusted contigs failure.

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FIX: clarification & refining the output of bgcSPAdes and coronaSPAdes.

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FIX: usage of >9 libraries in a single SPAdes run.

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FIX: improvements in spades-read-filter tool.

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SPAdes 3.15.2, 8 March 2021

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FIX: meta-viral pipeline bugs.

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FIX: coronaspades.py wrapper, copy proper files to the output folder.

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FIX: coronaSPAdes instability

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SPAdes 3.15.1, 18 February 2021

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FIX: Gap closer failure when using multiple libraries.

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FIX: Gap closer excessive memory consumption.

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IMPROVE: coronaSPAdes output.

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SPAdes 3.15.0, 11 January 2021

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NEW: CoronaSPAdes pipeline for assembly of full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data.

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NEW: Meta-Viral and RNA-Viral pipelines for identifying viral genomes for metagenomic and metatranscriptomic data.

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NEW: Novel algorithm for trusted contig usage.

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NEW: Switched to mimalloc memory allocator.

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NEW: PlasmidSPAdes and bgcSPAdes now support assembly graph as an input.

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CHANGE: Significant improvements and fixes for metaplasmid pipeline.

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CHANGE: Multiple performance improvements in simplification and repeat resolving procedures.

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DEPRECATED: Support for Lucigen NxSeq® Long Mate Pair reads.

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DEPRECATED: truSPAdes pipeline for TruSeq barcode assembly (still present in this release but no longer supported).

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SPAdes 3.14.1, 27 April 2020

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FIX: metaplasmidSPAdes contig output.

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FIX: read filtering binary.

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FIX: biosyntheticSPAdes pipeline fixed.

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FIX: fixed truSPAdes for Python 3.6+.

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FIX: bug in the internal mismatch correction procedure.

- -

FIX: Soft and hard-filtered transcripts are now copied to the output folder in rnaSPAdes.

- -

FIX: Several usability fixes in `spades.py'.

- -

FIX: meta-plasmid options added to the manual.

- -

FIX: several minor fixes in the user manual.

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SPAdes 3.14.0, 27 December 2019

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NEW: BiosyntheticSPAdes pipeline for predicting Biosynthetic Gene Clusters.

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NEW: Hybrid transcriptome assembly with rnaSPAdes.

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NEW: Plasmid detection from metagenomic samples.

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NEW: Special --isolate option for assembly of standard datasets with good coverage (>100x).

- -

NEW: Standalone tool for reads filtration based on k-mer coverage.

- -

NEW: Standalone tool for estimating approximate number of unique k-mers in reads.

- -

CHANGE: Improved SPAligner tool.

- -

CHANGE: Reworked python code, faster sequence transfer between different k-mer stages.

- -

CHANGE: Multiple performance improvements in graph construction and simplification procedures.

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FIX: BWA aligner failure for large graphs.

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FIX: Failure when additional paired-end libraries with reads shorter than final k-mer length are provided.

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SPAdes 3.13.2, 31 October 2019

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FIX: Incorrect k-mer size estimation in rnaSPAdes.

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SPAdes 3.13.1, 11 April 2019

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CHANGE: Removed BayesHammer from rnaSPAdes pipeline.

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CHANGE: Improved rnaSPAdes performance on large datasets.

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FIX: Failure in contig output in rnaSPAdes.

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SPAdes 3.13.0, 11 October 2018

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

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

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

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

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FIX: CQF and k-mer counting.

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SPAdes 3.12.0, 14 May 2018

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NEW: Support for merged paired-end reads.

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NEW: Experimental pipeline for metagenome hybrid assemblies.

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NEW: Standalone graph builder application.

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NEW: Standalone k-mer counting application.

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NEW: Standalone long read to graph aligner.

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CHANGE: Significant improvements in hybrid assembly pipeline.

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CHANGE: Faster read alignment using BWA.

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CHANGE: Improvements in metaSPAdes results.

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CHANGE: More sensitive results for rnaSPAdes.

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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.

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FIX: K value estimation for rnaSPAdes.

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

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SPAdes 3.11.1, 1 October 2017

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FIX: Handling spaces in path during mismatch correction.

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FIX: Python3 support in rnaSPAdes.

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FIX: K value estimation for long reads.

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FIX: Processing long reads alignments.

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SPAdes 3.11.0, 1 September 2017

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

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NEW: Coverage based isoform detection in rnaSPAdes.

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NEW: Reworked IonHammer read error correction module.

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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.

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SPAdes 3.10.1, 1 March 2017

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FIX: Build for MacOS.

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FIX: Minor bugs in hybridSPAdes pipeline.

- -

FIX: --continue option for metaSPAdes.

- -

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

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

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

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SPAdes 3.10.0, 27 January 2017

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

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NEW: Contigs and graph output in GFA format. - -

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

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CHANGE: Improvements in metagenomic pipeline.

- -

CHANGE: Improved isoform detection algorithm in rnaSPAdes.

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SPAdes 3.9.1, 4 December 2016

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FIX: macOS Sierra crash.

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SPAdes 3.9.0, 23 July 2016

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

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CHANGE: Improved memory consumption in metagenomic pipeline.

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FIX: Several minor bugs.

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SPAdes 3.8.2, 10 July 2016

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

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SPAdes 3.8.1, 8 June 2016

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FIX: plasmidSPAdes now works with PacBio/Nanopore reads.

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SPAdes 3.8.0, 1 June 2016

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

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CHANGE: Significant improvements in metaSPAdes performance.

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CHANGE: Improved running time and RAM consumption.

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SPAdes 3.7.1, 8 March 2016

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FIX: MismatchCorrector fixed for MaxOS.

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SPAdes 3.7.0, 24 February 2016

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NEW: metaSPAdes metagenomic pipeline.

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

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FIX: Multiple bug fixes.

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SPAdes 3.6.2, 20 November 2015

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

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FIX: Multithreaded MismatchCorrector.

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FIX: BayesHammer bug fixes.

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

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SPAdes 3.6.1, 4 October 2015

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

FIX: Multiple bugfixes.

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SPAdes 3.6.0, 17 August 2015

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

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

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

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CHANGE: Improvements and bugfixes in dipSPAdes.

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CHANGE: MismatchCorrector now uses bwa-mem.

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FIX: Bugfixes in MismatchCorrector.

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SPAdes 3.5.0, 7 December 2014

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NEW: New MismatchCorrector module.

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NEW: Support for Oxford Nanopore long reads.

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NEW: Support for Lucigen NxMate mate-pair libraries.

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

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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).

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FIX: Fixed FASTG format.

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SPAdes 3.1.1, 27 May 2014

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FIX: Several improvements in IonHammer.

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

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SPAdes 3.1.0, 27 May 2014

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

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NEW: Support for BAM files.

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CHANGE: Improved IonTorrent pipeline.

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

- -

FIX: Fixed dipSPAdes bugs and user interface.

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SPAdes 3.0.0, 29 December 2013

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NEW: Module for assemblying diplod highly polymorphic genomes.

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NEW: Support for PacBio reads.

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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.

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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.

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REMOVE: Rectangle graph repeat resolution module.

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SPAdes 2.5.1, 10 September 2013

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NEW: Python 3.2 and 3.3 compatibility.

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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.

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SPAdes 2.5.0, 2 July 2013

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

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

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CHANGE: Improved mismatch and indel rate.

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SPAdes 2.4.0, 26 February 2013

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NEW: Mismatch correction post-processing module.

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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).

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REMOVE: SAM-file generation.

- -

SPAdes 2.3.0, 30 October 2012

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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.

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REMOVE: No dependency from boost library.

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SPAdes 2.2.1, 20 August 2012

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

- - -

SPAdes 2.2.0, 2 August 2012

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NEW: No special binaries for different K values.

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NEW: Great improvements in error correction tool BayesHammer.

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

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CHANGE: Only 1 iteration of BayesHammer by default.

- -

NEW: Improved assembly quality.

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SPAdes 2.1.0, 28 May 2012

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NEW: Support multi-threading.

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NEW: Improved algorithms.

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NEW: Command-line interface. - -

CHANGE: Quality assesment separated from the core pipeline.

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REMOVE: No support for debian and RPM packages.

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SPAdes 2.0.1, 26 Apr 2012

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FIX: Quality tool fixed.

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SPAdes 2.0.0, 18 Apr 2012

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Initial release.

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- SPAdes website -

- - - - diff --git a/changelog.md b/changelog.md new file mode 100644 index 0000000000..49b4c7da67 --- /dev/null +++ b/changelog.md @@ -0,0 +1,468 @@ +# SPAdes Genome Assembler changelog + + +## SPAdes 3.15.5, 14 July 2022 + +- NEW: Support DNA HMMs. + +- FIX: use-after-free in PB aligner. + +- FIX: duplicated sequences in metaplasmid / metaviral mode. + + +## SPAdes 3.15.4, 1 February 2022 + +- FIX: MacOS Monterey memory limit failure. + +- FIX: upgrade pyyaml to run correctly with Python 3.10. + +- FIX: WSL for py2 check. + +- FIX: A few stability fixes. + + +## SPAdes 3.15.3, 22 July 2021 + +- FIX: trusted contigs failure. + +- FIX: clarification & refining the output of bgcSPAdes and coronaSPAdes. + +- FIX: usage of >9 libraries in a single SPAdes run. + +- FIX: improvements in `spades-read-filter` tool. + + +## SPAdes 3.15.2, 8 March 2021 + +- FIX: meta-viral pipeline bugs. + +- FIX: coronaspades.py wrapper, copy proper files to the output folder. + +- FIX: coronaSPAdes instability + + +## SPAdes 3.15.1, 18 February 2021 + +- FIX: Gap closer failure when using multiple libraries. + +- FIX: Gap closer excessive memory consumption. + +- IMPROVE: coronaSPAdes output. + + +## SPAdes 3.15.0, 11 January 2021 + +- NEW: CoronaSPAdes pipeline for assembly of full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. + +- NEW: Meta-Viral and RNA-Viral pipelines for identifying viral genomes for metagenomic and metatranscriptomic data. + +- NEW: Novel algorithm for trusted contig usage. + +- NEW: Switched to [mimalloc](https://github.com/microsoft/mimalloc) memory allocator. + +- NEW: PlasmidSPAdes and bgcSPAdes now support assembly graph as an input. + +- CHANGE: Significant improvements and fixes for metaplasmid pipeline. + +- CHANGE: Multiple performance improvements in simplification and repeat resolving procedures. + +- DEPRECATED: Support for Lucigen NxSeq® Long Mate Pair reads. + +- DEPRECATED: truSPAdes pipeline for TruSeq barcode assembly (still present in this release but no longer supported). + + +## SPAdes 3.14.1, 27 April 2020 + +- FIX: metaplasmidSPAdes contig output. + +- FIX: read filtering binary. + +- FIX: biosyntheticSPAdes pipeline fixed. + +- FIX: fixed truSPAdes for Python 3.6+. + +- FIX: bug in the internal mismatch correction procedure. + +- FIX: Soft and hard-filtered transcripts are now copied to the output folder in rnaSPAdes. + +- FIX: Several usability fixes in `spades.py'. + +- FIX: meta-plasmid options added to the manual. + +- FIX: several minor fixes in the user manual. + + +## SPAdes 3.14.0, 27 December 2019 + +- NEW: BiosyntheticSPAdes pipeline for predicting Biosynthetic Gene Clusters. + +- NEW: Hybrid transcriptome assembly with rnaSPAdes. + +- NEW: Plasmid detection from metagenomic samples. + +- NEW: Special `--isolate` option for assembly of standard datasets with good coverage (>100x). + +- NEW: Standalone tool for reads filtration based on k-mer coverage. + +- NEW: Standalone tool for estimating approximate number of unique k-mers in reads. + +- CHANGE: Improved SPAligner tool. + +- CHANGE: Reworked python code, faster sequence transfer between different k-mer stages. + +- CHANGE: Multiple performance improvements in graph construction and simplification procedures. + +- FIX: BWA aligner failure for large graphs. + +- FIX: Failure when additional paired-end libraries with reads shorter than final k-mer length are provided. + + +## SPAdes 3.13.2, 31 October 2019 + +- FIX: Incorrect k-mer size estimation in rnaSPAdes. + + +## SPAdes 3.13.1, 11 April 2019 + +- CHANGE: Removed BayesHammer from rnaSPAdes pipeline. + +- CHANGE: Improved rnaSPAdes performance on large datasets. + +- FIX: Failure in contig output in rnaSPAdes. + + +## 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 assessment 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.