Genome Assembler

ITMO de novo Genome Assembler version 0.1.5 (build 287, June 4, 2016) is available.

It can assemble paired reads into contigs as well as not paired.
Assembler can work with Illumina reads as well as Ion Torrent reads (with indel errors).
Assembler can be started from command line as well as from simple and clear graphical user interface:
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Download links:

JRE 1.6 or higher is required for running the assembler (you can download it here).
No other installations are required, just download and run the assembler.

How to run the assembler:
On UNIX-like OS first run chmod +x itmo-assembler.sh and then run ./itmo-assembler.sh.
On Windows simply run itmo-assembler.bat.
On other platforms use java -jar itmo-assembler.jar.

After running this command the graphical user interface will arise.
If you want to work with the assembler in command line, add option -h to the command and the assembler prints the instruction how to start the assembly process.

Before running the assembler please make sure that there is enough free space on your hard drive. The assembler does not remove temporal files in order to be able to continue running from any stage.

Previous versions of assembler can be found here: genome.ifmo.ru/files/software/assembler.
You may download nightly builds here: genome.ifmo.ru/files/software/assembler/nightly.