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Comparing de novo assemblers for metagenomic data obtained from Medium- Length sequencing technologies
Transcript of Comparing de novo assemblers for metagenomic data obtained from Medium- Length sequencing technologies
Bioinformatics Research Lab. CONCLUSION: Merging two assemblies at a time FUTURE WORK Use a simulation approach Exploring the parameter space for each assembler REFRENCES: 21.Gilbert, J.A., Thomas, S., Cooley, N.A., et al. Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters. Environmental Microbiology 11, 1 (2009), 111-125
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20.Miller, R.T., Christoffels, A.G., Gopalakrishnan, C., et al. A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge Base. Genome Research 9, 11 (1999), 1143-1155. Thanks for your attention. -Six Medium-Length assemblers
-All were run under default parameters
-Two sets of parameters were used to evaluate the assemblers:
Basic assembly metrics
assemler's performance Overal assembly size
Number of major contigs
Average contig size
N50 and N80 values Newbler
All the remaining assembler preformed almost as well No songle assembler petrformed best in all our criteria