https://github.com/applicativesystem/genome-size-estimates
estimating the genome size from illumina genome-seq and plotting the genome size.
https://github.com/applicativesystem/genome-size-estimates
bioinformatics genome-analysis genome-size genome-size-estimation illumina illumina-sequencing rlanuage rscript
Last synced: 6 months ago
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estimating the genome size from illumina genome-seq and plotting the genome size.
- Host: GitHub
- URL: https://github.com/applicativesystem/genome-size-estimates
- Owner: applicativesystem
- License: mit
- Created: 2024-08-19T18:58:49.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-09-12T08:04:53.000Z (about 1 year ago)
- Last Synced: 2024-12-16T02:12:09.011Z (10 months ago)
- Topics: bioinformatics, genome-analysis, genome-size, genome-size-estimation, illumina, illumina-sequencing, rlanuage, rscript
- Language: Shell
- Homepage:
- Size: 3.91 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# illumina-genome-size
estimation of the genome size for the illumina reads, only for the pre-screening purposes. if you have multiple illumina reads from the miseq, nextseq, and other illumina platform a short function to estimate the genome size. You can also write using the pillow library in python but i want to write today R. If you want me to write in python then leave a comment. give the fastq reads directory path and it will output calling a R function with publication ready figures.
> source the R function
```
#!/usr/bin/R
# -*- coding: utf-8 -*-
# Author: Gaurav
# date: 2023-10-23
stacking_option <- function(){
library(dplyr)
library(magick)
image_path <- character(length(list.files(path=".", pattern="*.png")))
for (i in seq_along(list(path=".", pattern="*.png"))){
image_path[i] <- paste0(getwd(),"/",list.files(path=".", pattern="*.png")[i])
a <- image_path[1]
b <- image_path[2]
c <- image_path[3]
d <- image_path[4]
image_write(image_append(c(a,b,c,d), stack=TRUE), "genome_estimation.png")
}
}
```
Gaurav Sablok \
University of Potsdam \
Potsdam,Germany