SPAdes 3.13.0

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.
REMOVE: dipSPAdes module.

SPAdes 3.12.0

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

FIX: Handling spaces in path during mismatch correction.
FIX: Python3 support in rnaSPAdes.
FIX: K value estimation for long reads in rnaSPAdes.
FIX: Processing long reads alignments.

SPAdes 3.11.0

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

FIX: Build for MacOS #12
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: Assertionpath.Length() > 0' failed in metaSPAdes.

SPAdes 3.10

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 3.9.0

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

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

SPAdes 3.8.1

FIX: plasmidSPAdes now works with PacBio/Nanopore reads.

SPAdes 3.8.0

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.