De novo assembly of single-cell bacterial genomes

In case of uncultured bacterial genome, NGS sequencers don't archive sequencing yet.

However, the multiplie displacement amplification (MDA, Go to Wikipedia and See this paper) method can be available.

MDA method is useful at the single cell but it might encounter amplification bias and chimeras.

Amplification bias is caused from the irregular coverage of amplified sequences and chimeras occur due to low sequence coverage. Most of standard assemblers use uniform coverage, so they can produce lots of erroneous contigs in case of a single cell assembly.

This paper introduces the specialized software tool for assembling single cell of uncultured bacteria.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets:

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

Nature Biotechnology 29, 915 (2011).
doi:10.1038/nbt.1966

Authors: Hamidreza Chitsaz, Joyclyn L Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L Dupont, Jonathan H Badger, Mark Novotny, Douglas B Rusch, Louise J Fraser, Niall A Gormley, Ole Schulz-Trieglaff, Geoffrey P Smith, Dirk J Evers, Pavel A Pevzner & Roger S Lasken