Releases: ablab/spades
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.