Genomer estimates the size of their sequencing data using three different algorithms and allows users to interact with the resulted models and compare between the results of the algorithms
Below is a list of algorithms included:
- Simple Counting Method - Simply counts the number of k-mers
- Peak K-mer Identifying Method - Identifies the peak of the k-mer distribution and estimates the size of the genome
- GenomeScope - Estimates the overall characteristics of a genome
Genomer takes in a histogram of k-mer frequencies as its input. You can use tools such as Jellyfish to compute the histogram. Below is an example command of running Jellyfish:
jellyfish count -m 21 -s 100M -t 10 -C reads.fasta && jellyfish histo -t 10 reads.jf > reads.histo
To run Genomer, simply run the following command in an R session (replace <GENOMER_DIR> with your own directory of Genomer):
shiny::runApp('<GENOMER_DIR>')