Here, we provide an online implementation of our previously described fragment assembly algorithm. To run the program, please upload your read file in FASTQ format and enter the number of iterations you would like to perform. You can find a sample read file here. Average Mutual Information (AMI) vector length is fixed at 16. Current DAC-FS implementation requires single-end sequencing data. Paired-end version of this software is under development. Click below to access the program.
Workflow
- The program takes input reads and calculates their AMI profiles.
- These vectors are clustered using a combination of k-means and hierarchical clustering.
- Each cluster is processed to identify reads that overlap.
- A consensus sequence is obtained for overlapping reads.
- Reads that have not been aligned with any other reads and the newly generated consensus sequences are regarded as a new set of reads and the whole process is repeated in the next iteration.
- Consensus sequences obtained after the last iteration are reported as final contigs.
Hasan Otu, Ph.D.
Email: hotu2@unl.edu
Sree Krishna Chanumolu, Ph.D.
Email: instanceofsree@gmail.com
Electrical and Computer Engineering, University of Nebraska–Lincoln, 430F NH, Lincoln, NE 68588-0511
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