Open Access Research article

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic

Rachel Sealfon12*, Stephen Gire23, Crystal Ellis45, Stephen Calderwood45, Firdausi Qadri6, Lisa Hensley7, Manolis Kellis12, Edward T Ryan458, Regina C LaRocque45, Jason B Harris49 and Pardis C Sabeti238*

Author Affiliations

1 Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, MA, USA

2 Broad Institute of MIT and Harvard, Cambridge, MA, USA

3 Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA

4 Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA

5 Department of Medicine, Harvard Medical School, Boston, MA, USA

6 International Centre for Diarrheal Disease Research, Dhaka, Bangladesh

7 Viral Therapeutics, United States Army Institute of Infectious Disease, Fort Detrick, MD, USA

8 Department of Immunology and Infectious Diseases, Harvard School of Public Health, Cambridge, MA, USA

9 Department of Pediatrics, Harvard Medical School, Boston, MA, USA

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BMC Genomics 2012, 13:468  doi:10.1186/1471-2164-13-468

Published: 11 September 2012

Additional files

Additional file 1:

Table S1. Depth of coverage and number of reads for each sequencing lane.

Format: XLSX Size: 41KB Download file

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Additional file 2:

Figure S2. Quality score vs. sequencing cycle for each isolate.

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Additional file 3:

Figure S3. Example alignments to additional strains for the validation of SNPs and insertions/deletions identified in N16961* relative to the N16961 reference.

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Additional file 4:

Table S4. Corrections to the N16961 reference sequence.

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Additional file 5:

Figure S5. Read alignment at positions at which the O395* isolate differs from the corresponding reference sequence.

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Additional file 6:

Figure S6. Alignment of the seven sequenced isolates against the MJ-1236 reference genome.

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Additional file 7:

Table S7. Non-synonymous SNPs shared among Haitian and Dominican Republic isolates.

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Additional file 8:

Figure S8. Alignments of DR1 reads at the positions where DR1 and Haitian cholera isolates differ.

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Additional file 9:

Table S9. Counts of SNPs, insertions, and deletions identified in each isolate relative to the N16961 reference.

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Additional file 10:

Table S10. SNPs and indels in sequenced isolates.

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Additional file 11:

Table S11. List of strains included in phylogenetic analysis.

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