Sunday, October 30, 2011

Single cell genomics even has its own software: SmashCell

Somehow I was not aware of this software called SmashCell even though it came out a while ago.  But it is worth checking out if you are interested in single-cell genomics.  There is an open access paper describing the software: SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Single cell genomics is becoming more and more important in studies of environmental microbiology as well as other fields like cancer biology.  One of the challenges with single cell genomics is that the amplification processes used to make copies of the genome from single cells are not completely accurate or efficient so you frequently end up with partial, somewhat messed up samples of genomes.  If you then sequence these amplified genomes it can be hard to make sense out of the data.  Hopefully this software may be of use to some doing this type of work.

Note - for those interested in more see this PLoS One paper I am a coauthor on:

Assembling the Marine Metagenome, One Cell at a Time



1 comment:

  1. Along a similar line is velvet-sc with Euler error correction:
    http://bix.ucsd.edu/projects/singlecell/

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