Kmergenie
|
Application data |
|
| Created by | R. Chikhi, P. Medvedev |
|---|---|
| Biological application domain(s) | Genomic Assembly |
| Principal bioinformatics method(s) | Assembly |
| Technology | Illumina |
| Created at | Penn State University |
| Maintained? | Yes |
| Input format(s) | Fasta/Fastq |
| Output format(s) | HTML report |
| Programming language(s) | C++/Python/R |
Summary: KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.
"Error: no local variable "counter" was set." is not a number.
Description
Links
References
none specified
To add a reference for Kmergenie, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "Kmergenie" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
