[Rao]

http://www.cs.sunysb.edu/~skiena/shorty/

SHORTY
What is the status this tool...?

[SoftGenetics]

short read assembler

Hi you might wish to try the new assemblers in nextGENe which in addition to de novo assembly has a condensation tool which removes chemistry and instrument errors...it is faster and more accurate than the ones mentioned.

[nilshomer]

oops... found another useful thread with these suggestions:

* MIRA2 - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
* SHARCGS - De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.
* SSAKE - Version 2.0 of SSAKE (23 Oct 2007) can now handle error-rich sequences. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.
* VCAKE - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
* Velvet - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Anyone use more than one of these assemblers? I have low coverage with short solexa tags --> really just want to combine reads into longer reads.

Don't forgett ABySS out of BCGSC. ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research, 2009-June.

[michael_0214]

A Question for Shorty

Hi! A question for Shorty: When installing the Shorty, a mistake took place- configuration file needed, in this step:/build conf/conf-file bin/shorty-assembler. Can anyone give me a hand ? Thank you!