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.
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
FIX: meta-viral pipeline bugs.
FIX: coronaspades.py wrapper, copy proper files to the output folder.
FIX: coronaSPAdes instability
FIX: Gap closer failure when using multiple libraries.
FIX: Gap closer excessive memory consumption.
IMPROVE: coronaSPAdes output.
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).
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.
NEW: BiosyntheticSPAdes pipeline for predicting Biosynthetic Gene Clusters.
NEW: Hybrid transcriptome assembly with rnaSPAdes.
NEW: Plasmid detection from metagenomic samples.
--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.
FIX: Incorrect k-mer size estimation in rnaSPAdes.
CHANGE: Removed BayesHammer from rnaSPAdes pipeline.
CHANGE: Improved rnaSPAdes performance on large datasets.
FIX: Failure in contig output in rnaSPAdes.
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.
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).
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.
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.
FIX: Build for MacOS.
FIX: Minor bugs in hybridSPAdes pipeline.
--continue option for metaSPAdes.
--tmp-dir is now works correctly for MismatchCorrector.
Assertion `overlap <= k_' failed in rnaSPAdes and metaSPAdes.
Assertion `path.Length() > 0' failed in metaSPAdes.
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.
FIX: macOS Sierra crash.
NEW: rnaSPAdes pipeline for de novo transcriptome assembly from RNA-Seq data.
CHANGE: Improved memory consumption in metagenomic pipeline.
FIX: Several minor bugs.
FIX: Several minor bug-fixes for metaSPAdes and SPAdes pipelines.
FIX: plasmidSPAdes now works with PacBio/Nanopore reads.
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.
FIX: MismatchCorrector fixed for MaxOS.
NEW: metaSPAdes metagenomic pipeline.
CHANGE: improved performance for both error correction and assembly stages.
FIX: Multiple bug fixes.
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.
CHANGE: No misleading FASTG files, only assembly graph is saved in FASTG format.
FIX: Multiple bugfixes.
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.
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.
FIX: Several improvements in IonHammer.
FIX: Fixed a few minor bugs in repeat resolution and scaffolding.
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.
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
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.
NEW: Python 3.2 and 3.3 compatibility.
NEW: Possibility to continue SPAdes run starting from the last check-point with the
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.
NEW: Multiple paired-end and mate-pair libraries.
NEW: Recipe for assembling Illumina 2x150bp and 2x250bp reads.
CHANGE: Improved mismatch and indel rate.
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.
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.
Verification of expression 'v1 == conjugate(v2)' failed error.
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.
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.
FIX: Quality tool fixed.