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- MIRA
- Velvet
- ABYSS
- Using consed, including editing Mira assemblies
- ABI's SOLiD de novo pipeline
- Phred, Phrap, Consed, cross_match, daev
- Allpaths-LG
- Mosaik - A suite of alignment and reference-guided assembly tools.
- (Newbler, the Roche/454 assembler, is under 454 Analysis tools)
Transcriptome de novo assembly
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ABI pipelines
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