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Reducing assembly complexity of microbial genomes with single-molecule sequencing

Sergey Koren1*, Gregory P Harhay2, Timothy PL Smith2, James L Bono2, Dayna M Harhay2, Scott D Mcvey3, Diana Radune1, Nicholas H Bergman1 and Adam M Phillippy1

Author Affiliations

1 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA

2 USDA, ARS, Meat Animal Research Center, Clay Center, NE 68933, USA

3 USDA, ARS, Center for Grain and Animal Health Research, Manhattan, KS 66502, USA

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Genome Biology 2013, 14:R101  doi:10.1186/gb-2013-14-9-r101

Published: 13 September 2013

Additional files

Additional file 1:

Repeat Stats. Listing of repeat count and maximum repeat size for all complete genomes.

Format: XLSX Size: 63KB Download file

Open Data

Additional file 2:

Report.log.krona. An interactive Krona [35] chart detailing the expected number of gaps for all strains, species, genera, and so on under various coverage and chemistry scenarios.

Format: HTML Size: 9.2MB Download file

Open Data

Additional file 3:

ValidationResults. Reference-free assembly validation. The columns are as described in Table 2 with the addition of the max contig, unmated LAP score, FRC feature count, and ALE scores.

Format: XLSX Size: 212KB Download file

Open Data