HyDA 1.3.1 / Squeezambler 2.0.3
HyDA is a multipurpose assembler, particularly tested for single cell and normal multicell genome co-assembly
Squeezambler is a divide-and-conquer algorithm for economical sequencing and assembly of all distinct genomes in a bacterial sample. The key idea here is exploiting sparsity, which is the small number of distinct genomes (~1000) in comparison to the huge number of cells (~100 trillion).
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Narjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz,
De Novo Co-assembly of Bacterial Genomes from Multiple Single Cells,
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp 561-565, 2012
Bioinformatics. 2013 Aug 13. [Epub ahead of print]
Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.
Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.