Recommendation list

SOAPdenovo (PE)
Ray (PE)
Ray (SE)
Sprai
MIRA
SOAPdenovo scaf and GapCloser (PE)
Ray, GC_coverage_length plot, blastx Uniport and blastn NR (PE)
Annotation after assembling (PE)
Annotation after assembling (SE)

Related list

FastQC (PE)
Jellyfish (PE)
Jellyfish (SE)

Note "SE": For single-end read, "PE": For paired-end read, "GE": Genome explorer which is our original genome browser.
It is necessary to register to analyze your own data.
: The popular pipeline or the latest one that the developer recommend.
Notice: Unrecomend not a tool used by the pipeline but the workflow of the pipelie.

References:

• Nature. 2010 Jan 21;463(7279):311-7. doi: 10.1038/nature08696
• Nature. 2012 May 30;485(7400):635-41. doi: 10.1038/nature11119
• Science. 2013 Jan 25;339(6118):456-60. doi: 10.1126/science
• Nat Genet. 2010 Dec;42(12):1053-9. doi: 10.1038/ng.715