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SPAdes 3.11 is released!

Submitted by andrey on 4 Sep 2017, Mon, 11:40

A new version of SPAdes if finally out. In this release you will see many nice improvements, such as

  • Reworked IonHammer module
  • Major improvements in metaSPAdes pipeline
  • Support for strand-specific data and coverage-based isoform detection in rnaSPAdes
  • exSPAnder repeat resolution is improved in terms of both performance and repeat resolution accuracy
  • Better RAM consumption and running time in general
  • Improved careful mode for isolate datasets 
  • Several important bug-fixes

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!

 

 

QUAST 4 with Icarus assembly browser is out

QUAST 4.0 introduces Icarus - a novel assembly genome browser.

We also present a new misassembly detection algorithm that minimises the number of false positives (erroneously detected misassemblies) in cases of multiple ambiguous mappings of contig fragments.

For the full lest of changes, see quast.bioinf.spbau.ru/changes

 
 

Please download the tool of use the web interface: quast.bioinf.spbau.ru

 

Icarus: visualizer for de novo assembly evaluation

Dear users! Our website moved to quast.sf.net! New Icarus page is here.

 
Icarus is a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on QUAST genome quality assessment tool. Icarus consists of two major contig viewers:
  • Contig alignment viewer – draws contigs according to their mapping to the reference genome, visualizes misassemblies and similarities between assemblies. The viewer can visualize genes, operons, and reads coverage distribution along the genome, if any of those were provided to QUAST.
  • Contig size viewer – draws contigs ordered from longest to shortest, highlights N50, N75 (NG50, NG75) and long contigs larger than a user-specified threshold.
 
You can try Icarus online at http://quast.bioinf.spbau.ru/ -- upload your assemblies, get regular QUAST report and press the Icarus: contig browser link.
 
Icarus is distributed as a command-line tool within QUAST package since version 4.0.

 

GitHub     Full manual (Icarus specific section: output description)

 

Citation:

Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, Alexey Gurevich,
Icarus: visualizer for de novo assembly evaluation,
Submitted (2016).

 

Examples of Icarus output on 3 datasets generated with QUAST v4.0

icarus_al_viewer
 
 
 
icaurs_metagnome_menu
 
 
icarus_contig_size_viewer
 
 
 
Please help us to make Icarus better by sending your comments, bug reports, and suggestions to quast.support@bioinf.spbau.ru

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

 

MetaSPAdes

metaSPAdes is now released as a part of SPAdes 3.7

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

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