SPAdes 3.15.0

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 NxSeqВ® Long Mate Pair reads.
DEPRECATED: truSPAdes pipeline for TruSeq barcode assembly (still present in this release but no longer supported).

SPAdes 3.14.1

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

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: Major performance improvements and memory consumption reduction in graph construction, simplification procedures and throughout the whole pipeline.
FIX: BWA aligner failure for large graphs.
FIX: Failure when additional paired-end libraries with reads shorter than final k-mer length are provided.

SPAligner: early access version

SPAligner is a standalone tool for aligning long diverged molecular (both nucleotide and amino acid) sequences against assembly graphs produced by the popular short-read assemblers.
This is an early preview version of SPAligner to supplement the publication.

SPAdes 3.14-dev for CAMI submission

This is early pre-release version of SPAdes 3.14 used for CAMI 2 challenge submission

cloudSPAdes: ISMB version

Description

cloudSPAdes is a module of the SPAdes assembler aimed at genome assembly from the data generated using Synthetic Long Read (SLR) technologies, such as 10X Genomics Chromium or UST TELL-Seq.

Availability

cloudSPAdes will be available soon as a part of SPAdes package. For now one can download, build, and try pre-release version of SPAdes package included in this repository.

Support

If you have a problem running SPAdes you can look for a similar issue on our GitHub repository, create a new one or write us via e-mail: spades.support@cab.spbu.ru.

Early access version to supplement ISMB submission

HMM PathRacer: early access version

Early access version of HMM PathRacer to supplement RECOMB-SEQ talk.
Preprint: https://www.biorxiv.org/content/10.1101/562579v1

SPAdes 3.13.1

CHANGE: Removed BayesHammer from rnaSPAdes pipeline.
CHANGE: Improved rnaSPAdes performance on large datasets.
FIX: Failure in contig output in rnaSPAdes.

metaplasmidSPAdes: early preview version

This is an early preview version of metaplasmidSPAdes pipeline to supplement the publication.

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.