Team I Genome Assembly Group: Difference between revisions
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===Data=== | ===Data=== | ||
We downloaded 258 Klebsiella spp. (paired-end reads; 250 base pairs in length) from [https://www.ncbi.nlm.nih.gov/sra/ NCBI SRA database]. | |||
=='''Objective'''== | =='''Objective'''== | ||
Revision as of 09:26, 27 February 2018
The group is conducting its discussions, planning, etc. on the Open Academic Environment. Our group is public.
Introduction
Background
Figure 1. Bacterial Genomics [1]
Bacterial genomics is the discipline concerning the genome of a bacteria and includes all hereditary information regarding that bacteria. Bacterial genomics helps study bacterial evolution as well as determine the causative agent in disease outbreaks. Bacterial genomics helps identify bacterial pathogens (and antibiotic resistance) and how these pathogens interact with their host. Deciphering bacterial genomes is in great need.
Figure 2. Klebsiella (http://healthcare.bioquell.com)
Features of Klebsiella[2,3]: a) Gram negative, non-motile, straight rods, Capsule forming; b) Singly, in pairs or short chains; c) Both respiratory and fermentative metabolism, facultative (metablolism switching based on environment); d) Oxidase negative; e) GC content: ~57%
Data
We downloaded 258 Klebsiella spp. (paired-end reads; 250 base pairs in length) from NCBI SRA database.
Objective
Methods
Pipeline
Pre-processing
Assembly
Algorithms
Burrows–Wheeler Transform(BWT)
De Bruijn graph
Discussion
Conclusions
References
1. Perna, Nicole T., Guy Plunkett III, Valerie Burland, Bob Mau, Jeremy D. Glasner, Debra J. Rose, George F. Mayhew et al. "Genome sequence of enterohaemorrhagic Escherichia coli O157: H7." Nature 409, no. 6819 (2001): 529.
2. Bergey, David Hendricks, Robert Stanley Breed, Everitt George Dunne Murray, and A. Parker Hitchens. Bergey's manual of determinative bacteriology. Baltimore: Williams & Wilkins, 1934.
3. Wikipedia contributors, "Klebsiella," Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Klebsiella&oldid=821116734 (accessed February 27, 2018).