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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.

SPAdes 3.1.1: a bug fix release

Introduced several improvements in IonHammer; fixed minor bugs in repeat resolution and scaffolding.


ExSPAnder won the Outstanding Paper Award at ISMB!

The paper "ExSPAnder: a universal repeat resolver for DNA fragment assembly" won the Outstanding Student Paper award at ISMB 2014! Congratulations to Andrey D. Prjibelski and Irina Vasilinetc.

The award is given to the undergraduate, Master’s or PhD student who presents the most thought-provoking or original paper at the Conference, as judged by the panel of experts.

ISMB 2014, the conference on computational biology took place in Boston at July 11–15, 2014. In addition to the paper, the Lab also presented a poster on SPAdes 3.0: "New Features in SPAdes Genome Assembler".

Вышла публикация о новом алгоритме разрешения повторов ExSPAnder

Последняя версия геномного сборщика SPAdes использует новый универсальный алгоритм разрешения повторов ExSPAnder. Этот метод точно работает с несколькими библиотеками парных ридов как проектах секвенирования по одной клетке, так и в случае культивируемых клеток.

Теперь статья об алгоритме обуликована в журнале «Биоинформатика»:


SPAdes 3.1 is out!

We just released SPAdes 3.1 with several improvements and bugfixes:
- Mate-pairs only assembly (for high-quality mate-pair libraries like Illumina NexteraMP)
- Unmapped BAM file support (like the ones produced from Torrent Server)
- Improved IonTorrent pipeline
- Fixed dipSPAdes bugs and user interface
- Better assemblies with mate-pair libraries
- Improved performance of repeat resolution module
Download new version at

SPAdes on BaseSpace: one-click assembly on cloud

Illumina announced SPAdes realease in their cloud-computing environment BaseSpace.

BaseSpace is the first cloud environment directly integrated into Illumina industry-leading sequencing platform. It allows sequencing labs easily and securely analyze, archive, and share sequencing data.

Now SPAdes assembler is integrated into the platform and can be used as a one-button solution for de novo assembly of small genomes. The output includes assembly quality statistics provided by QUAST.

QUAST 2.3 released

Long-awaited contig alignment plots (see an example below), updated misassemblies detection logic, full report in PDF format, and many other features included!

See Changes for for a full list of new features and fixed bugs.

See new version of Manual including new options and reports descriptions and FAQ section.

All other news and useful links are presented on QUAST page.
You can download QUAST 2.3 and previous versions here.

SPAdes 3.0 is out

Now with support for IonTorrent, PacBio, module for highly polymorphic diploid genomes and many other new features. Check out the details here.

Вышло обновление ассемблера: SPAdes 2.5.1

Доступна новая версия ассемблера SPAdes — 2.5.1.


  • более дружественные отчеты об ошибках,
  • меньше мисассемблов на данных по одной клетке с низким покрытием,
  • сокращено потребление памяти на этапе исправления ошибок в ридах.

Новая функциональность:

  • запуск с контрольных точек: ассемблер можно перезапустить после неудачного запуска без необходимости проходить все этапы с нуля; 
  • автоматическая подборка длины k-меров для стандартных данных (определяется по максимальной длине рида).

SPAdes 2.5.1 можно скачать здесь.

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