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SPAdes 3.9: introducing rnaSPAdes transcriptome assembler

 

We are happy to announce that we have just released new SPAdes 3.9.0. In this version, we have included rnaSPAdes – a de novo transcriptome assembler for RNA-Seq data.

SPAdes 3.8 is out!

 

 


 

 

 

We have just released a new version of SPAdes, which includes the following features and modifications:

  • plasmidSPAdes – a pipeline for extracting and assembling plasmids from WGS data;
  • major improvements in metaSPAdes;
  • several performance improvements.

Try SPAdes 3.8 now!

 

 

SPAdes 3.7 with metaSPAdes is out

We are happy to announce that we have just released new SPAdes 3.7.0. This version includes metaSPAdes metagenomic pipeline and many other improvements and fixes.

Please note that SPAdes is not intended for large genomes (e.g. mammalian size genomes). Should you decide to use SPAdes for a larger genome, please be aware that you are doing it at your own risk.

SPAdes version 3.7.0 is released under GPLv2 and openly available for download from http://bioinf.spbau.ru/en/spades.


Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve SPAdes. If you have any troubles running SPAdes, please provide us with the files params.txt and spades.log from the output directory. Address for communications: spades.support@bioinf.spbau.ru.

 

 

 

rnaQUAST is released

rnaQUAST is a tool for evaluating quality of transcriptome assemblies using reference genome and gene database. You can download here the first stable release

SPAdes updated to v. 3.6.2

A bug-fix release SPAdes 3.6.2 is available. Please consider updating SPAdes: http://bioinf.spbau.ru/en/spades

 

SPAdes 3.6.1 is available! A bug-fix release.

SPAdes 3.6.1 is available! 

A bug-fix release. 

Please consider updating SPAdes: http://bioinf.spbau.ru/en/spades

QUAST 3.1 is out - even better, faster, much lighter installation package, and brand new visualizations in MetaQUAST

QUAST 3.1 released! Even better, faster, and much lighter than QUAST 3.0.

  • Significantly reduced size of the installation package
  • MetaQUAST includes Krona charts, heatmaps, and many other new features
http://quast.bioinf.spbau.ru/metaquast/metahit/summary/report.html

SPAdes 3.6: better performance + truSPAdes for TruSeq long reads

SPAdes 3.6 is out!

NEW: Added truSPAdes – an assembler for short reads produced by Illumina TruSeq Long Read technology.

Changes:

  • Better running time, less RAM consumption and improved results for BayesHammer error correction module.
  • Improvements and bugfixes in repeat resolution and scaffolding modules.
  • Improvements and bugfixes in dipSPAdes.
  • MismatchCorrector now uses bwa-mem.
  • Bugfixes in MismatchCorrector.

QUAST 3 is out!

Brand new version of QUAST is released!

  • Faster: 5x–100x more running w/o reference; running in parallel with large references; new spead-up options: --no-check, --no-gc, --no-snps, --fast
  • Better: more accurate missasembly detection algorithm, new metrics and reports
  • New MetaQUAST: better contig binning, multi-reference reports, interspecies translocations

Download here. Check the full list of changes here.

SPAdes 3.5 is out: Nanopores, Lucigen NxMate mate-pairs, new mismatch correction

New SPAdes 3.5 is out!

This release includes new mismatch correction module, support for Oxford Nanopore and Lucigen NxMate mate-pair libraries, possibility to specify coverage cutoff, improved performance and several fixes.

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