(转)8 reviews about de novo genome assembly

转自:http://dskernel.blogspot.com/2012/04/8-reviews-about-de-novo-genome-assembly.html

8 reviews about de novo genome assembly

 

1.

 

Monya Baker (Editor at Nature)

De novo genome assembly: what every biologist should know

Nature Methods 9, 333–337 (2012) doi:10.1038/nmeth.1935

http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html

 

2.

 

Paul Flicek & Ewan Birney (European Bioinformatics Institute)

Sense from sequence reads: methods for alignment and assembly

Nature Methods 6, S6 - S12 (2009) 

http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1376.html

 

3.

 

Mihai Pop

(Center for Bioinformatics and Computational Biology, University of Maryland)

Genome assembly reborn: recent computational challenges

Brief Bioinform (2009) doi: 10.1093/bib/bbp026

http://bib.oxfordjournals.org/content/early/2009/05/29/bib.bbp026.full

 

4.

 

Ewan Birney (European Bioinformatics Institute)

Assemblies: the good, the bad, the ugly

Nature Methods 8, 59–60 (2011) doi:10.1038/nmeth0111-59

http://www.nature.com/nmeth/journal/v8/n1/abs/nmeth0111-59.html

 

5.

 

Jason R. Miller, Sergey Koren, and Granger Sutton

(J. Craig Venter Institute)

Assembly Algorithms for Next-Generation Sequencing Data

Genomics. 2010 Jun;95(6):315-27. Epub 2010 Mar 6.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/?tool=pubmed

 

6.

 

Phillip E C Compeau, Pavel A Pevzner & Glenn Tesler

(University of California San Diego)

How to apply de Bruijn graphs to genome assembly

Nature Biotechnology 29, 987–991 (2011) doi:10.1038/nbt.2023

http://dx.doi.org/doi:10.1038/nbt.2023

 

7.

 

Michael C. Schatz, Arthur L. Delcher and Steven L. Salzberg

(Center for Bioinformatics and Computational Biology, University of Maryland)

Assembly of large genomes using second-generation sequencing

Genome Res. 2010. 20: 1165-1173 doi:10.1101/gr.101360.109

http://dx.doi.org/doi:10.1101/gr.101360.109

 

8.

 

Can Alkan, Saba Sajjadian & Evan E Eichler

(Department of Genome Sciences, University of Washington)

Limitations of next-generation genome sequence assembly

Nature Methods 8, 61–65 (2011) doi:10.1038/nmeth.1527

http://www.nature.com/nmeth/journal/v8/n1/full/nmeth.1527.html

9.

Steven L. Salzberg and James A. Yorke
(University of Maryland)
Beware of mis-assembled genomes
Bioinformatics (2005) 21 (24): 4320-4321. doi: 10.1093/bioinformatics/bti769
http://dx.doi.org/doi:10.1093/bioinformatics/bti769