SPAdes Genome Assembler
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 NxSeqВ® 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. 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 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.
This is early pre-release version of SPAdes 3.14 used for CAMI 2 challenge submission
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.
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.
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: [email protected].
Early access version to supplement ISMB submission
Early access version of HMM PathRacer to supplement RECOMB-SEQ talk. Preprint: https://www.biorxiv.org/content/10.1101/562579v1
CHANGE: Removed BayesHammer from rnaSPAdes pipeline. CHANGE: Improved rnaSPAdes performance on large datasets. FIX: Failure in contig output in rnaSPAdes.