### Install GenomeScope 2.0 R Package Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Installs the GenomeScope 2.0 R package using the provided installation script. This should be run after cloning the repository. ```bash Rscript install.R ``` -------------------------------- ### GenomeScope Example Run Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md An example of running GenomeScope with specific parameters, using a provided histogram file for Arabidopsis F1 data. The output will be saved to the 'output' directory. ```bash $ /PATH/TO/genomescope.R -i ara_F1_21.hist -o output -k 21 ``` -------------------------------- ### Install R Packages with Conda Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Installs necessary R packages, including argparse and minpack.lm, using conda. Ensure you have a working R environment. ```bash conda install -c conda-forge r-base r-minpack.lm r-argparse ``` -------------------------------- ### Run GenomeScope Analysis Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Executes the GenomeScope analysis from the command line. Requires the input histogram file, output directory, and k-mer length. Ensure genomescope.R is in your PATH. ```bash $ genomescope.R -i histogram_file -o output_dir -k k-mer_length ``` -------------------------------- ### Count k-mers with KMC Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Use this command to count k-mers with KMC. Adjust memory (-m) and threads (-t) based on your server. The k-mer length (-k) may need adjustment for low coverage or high error rates. Bounds (-ci, -cs) exclude k-mers outside the specified counts. FILES should be a file listing input FASTQ files. ```bash mkdir tmp ls *.fastq > FILES kmc -k21 -t10 -m64 -ci1 -cs10000 @FILES reads tmp/ ``` -------------------------------- ### Export k-mer histogram with Jellyfish Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Export the k-mer count histogram using Jellyfish. Scale the thread count (-t) according to your server. ```bash jellyfish histo -t 10 reads.jf > reads.histo ``` -------------------------------- ### Google Analytics Initialization Source: https://github.com/tbenavi1/genomescope2.0/blob/master/header.html Initializes Google Analytics for tracking page views. This script should be included in the header of your HTML file. ```javascript GenomeScope GenomeScope (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-73314063-1', 'auto'); ga('send', 'pageview'); ``` -------------------------------- ### Clone GenomeScope 2.0 Repository Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Downloads the GenomeScope 2.0 source code from GitHub and navigates into the project directory. ```bash git clone https://github.com/tbenavi1/genomescope2.0.git cd genomescope2.0/ ``` -------------------------------- ### Display Recent User Datasets Source: https://github.com/tbenavi1/genomescope2.0/blob/master/header.html Retrieves and displays a list of the user's most recent datasets from cookies. It calculates and shows the time elapsed since each dataset was added. ```php 20) { $start_at = $arrlength - 20; } for($x = $start_at; $x < $arrlength; $x++) { $seconds_ago = time() - $my_datasets[$x]["date"]; $time_ago = $seconds_ago; if ($seconds_ago > 60) { $minutes_ago = $seconds_ago/60; if ($minutes_ago > 60) { $hours_ago = $minutes_ago/60; if ($hours_ago > 24) { $days_ago = $hours_ago/24; $time_ago = "" . floor($days_ago) . " days"; } else { $time_ago = "" . floor($hours_ago) . " hours"; } } else { $time_ago = "" . floor($minutes_ago) . " minutes"; } } else { $time_ago = "" . floor($seconds_ago) . " seconds"; } echo "* [" . $my_datasets[$x]["description"] . " (" . $time_ago . " ago)](analysis.php?code=" . $my_datasets[$x]["codename"] . ")\n"; } ?> ``` -------------------------------- ### Count k-mers with Jellyfish Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Use this command to count k-mers with Jellyfish. Adjust memory (-s) and threads (-t) based on your server. Use canonical k-mers (-C) as reads come from both DNA strands. The k-mer length (-m) may need adjustment for low coverage or high error rates. ```bash jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf ``` -------------------------------- ### Export k-mer histogram with KMC tools Source: https://github.com/tbenavi1/genomescope2.0/blob/master/README.md Export the k-mer count histogram using KMC tools. The upper bound (-cx) sets the cutoff for the histogram. ```bash kmc_tools transform reads histogram reads.histo -cx10000 ``` -------------------------------- ### GenomeScope 2.0 Model Formula Source: https://github.com/tbenavi1/genomescope2.0/blob/master/user_data/example2/model.txt The core statistical formula used in the GenomeScope 2.0 model, defining the relationship between variables. ```R y ~ ((2 * (1 - d) * (1 - (1 - r)^k)) * dnbinom(x, size = kmercov/bias, mu = kmercov) * length + ((d * (1 - (1 - r)^k)^2) + (1 - 2 * d) * ((1 - r)^k)) * dnbinom(x, size = kmercov * 2/bias, mu = kmercov * 2) * length + (2 * d * ((1 - r)^k) * (1 - (1 - r)^k)) * dnbinom(x, size = kmercov * 3/bias, mu = kmercov * 3) * length + (d * (1 - r)^(2 * k)) * dnbinom(x, size = kmercov * 4/bias, mu = kmercov * 4) * length) ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.