Estimate genome size of polyploid species using k-mer frequencies
Usage:
Upload results from running Jellyfish. Example: javanica_tetraploid.histo potato_tetraploid.histo wheat_hexaploid.histo strawberry_octoploid.histo Chinese_sturgeon_octoploid.histo
Instructions for running Jellyfish:
- Download and install jellyfish from: http://www.genome.umd.edu/jellyfish.html#Release
-
Count k-mers using jellyfish:
$ jellyfish count -C -m 21 -t 1 -s 5G *.fastq -o reads.mer
Note you should adjust the memory (-s) and threads (-t) parameter according to your server. This example will use 1 threads and 5GB of RAM. The k-mer length (-m) may need to be scaled if you have low coverage or a high error rate.
-
Generate the k-mer count histogram file:
$ jellyfish histo -h 30000000 -t 10 -o reads.histo reads.mer
Again the thread count (-t) should be scaled according to your server.
- Upload reads.histo to findGSEP
Instructions for install findGSEP package:
-
Install devtools package(Under R environment):
$ install.packages("devtools") -
Install directly from github
$ devtools::install_github("sperfu/findGSEP")
Estimate genome size from sequencing reads using a k-mer-based approach
Contact Us
Contact us if you have any questions about the usage of this website.
Contact information
Laiyi Fu & Hequan Sun
Email: fulaiyi@xjtu.edu.cn & hequan.sun@xjtu.edu.cn
Github Page: Github web
Cite:
Please consider to cite our paper if you use findGSEP in your research.
Paper title: findGSEP: a web application for estimating genome size of polyploid species using k-mer frequencies
Corresponding author e-mail: hequan.sun@xjtu.edu.cn
Corresponding author website: Website
Acknowledgement
We would like to thank XiaMeng Wei(Xijing University) for helpful discussion and logo design.