SSAKE protocols

SSAKE specifications

Information


Unique identifier OMICS_00033
Name SSAKE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Rene Warren <>

Publication for SSAKE

SSAKE IN pipeline

2009
PMCID: 2772860
PMID: 19835600
DOI: 10.1186/1471-2164-10-479

[…] repetitive elements using repeatmasker [24] with default options, species chicken, and reads containing repetitive elements were removed. remaining reads were assembled to short read contigs using ssake [12] and the default parameters. the data set containing contigs larger than 50 bp are referred to reference genome c50., the short read contigs (c50) were mapped on the chicken genome […]

SSAKE institution(s)
British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, Canada; J. Craig Venter Institute, Rockville, MD, USA

SSAKE reviews

 (2)
star_border star_border star_border star_border star_border
star star star star star

Ahmed Nabiel

star_border star_border star_border star_border star_border
star star star star star
Desktop
The best short read assembler I could find!
Anonymous user #48's avatar image No country

Anonymous user #48

star_border star_border star_border star_border star_border
star star star star star
Desktop
Ssake is super easy to use and produces accurate results.
It is lightweight and has no dependencies, I highly recommend it. Because it uses coverage info, assemblies are stratified which makes it also suitable for transcriptome and meta genome assemblies. It is not as greedy as most people report, the correct path is chosen no based on longest overlap, but coverage and reads having a matching pairing partner already assembled