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SPAdes Genome Assembler changelog

SPAdes 4.0.0, 3 June 2024

  • SPAdes now supports NCBI SRA files as input;
  • Reworked and improved documentation: ablab.github.io;
  • PathRacer - a tool for mapping HMMs to assembly grpah - is now released as a part of SPAdes package;
  • BinSPreader (metagenomic binning refiner) is also released inside SPAdes package;
  • New gfa-split tool for splitting assembly graph into components;
  • New wasterwaterSPAdes mode for quantitative assessment of SARS-CoV-2 strains in waste water samples;
  • Python3.8 is now a minimal required version, python2 is deprecated;
  • Native support for running on Apple Silicon processors;
  • Native support for running on aarch64/linux;
  • Binaries are now built using ManyLinux 2.28. SPAdes binaries should be compatible with systems using glibc 2.28 and newer including ALT Linux 10+, RHEL 9+, Debian 11+, Fedora 34+, Mageia 8+, Photon OS 3.0 with updates, Ubuntu 21.04+. In case of any problems we recommend building from sources.
  • Allow external projects integration with SPAdes. Projects could be integrated directly with SPAdes codebase or use SPAdes libraries. Contact us for technical details.
  • SPAdes outputs assembly graph in GFA v1.2 format by default, older v1.1 format is also available;
  • SPAdes tags circular paths in assembly graph with TP:Z:circular flag;
  • SPAdes internally supports 0 bp overlap graph and graphs with variable overlaps in vertices (e.g. multiplex de Bruijn graphs). Some SPAdes standalone tools allow use of such graphs as input.
  • SPAdes now uses zlib-ng for faster gzip decompression of input files;
  • Fixed compilation with gcc 13;
  • Use SPOA for long reads consensus;
  • Parallel & improved GapCloser algorithm;
  • Faster graph simplification;
  • Removed deprecated truSPAdes functionality;
  • Lots of other fixes and improvements.

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 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.