There is a growing list of single-cell analysis software as well as tutorials and workshop materials here:
Contributions of additional software and materials are appreciated.
Single-Cell Omics issue was just published.
This has been added.
The BBMap package contains a couple of tools that are useful for single-cell studies, particularly BBNorm for normalization of the raw reads prior to assembly, and CrossBlock for eliminating cross-contamination after assembly which is common in multiplexed bacterial libraries. Each has a manual in /bbmap/docs/guides/. It also contains Tadpole, which is an assembly and error-correction program; while there are many error-correction tools, Tadpole is specifically designed to work with MDA'd single-cell data, unlike most others.
I want to make sure that we get the descriptions right, so perhaps you can add via a pull request?
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