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https://github.com/loukesio/barcosim
BarcoSim, a specialized R package designed for simulating barcoded amplicon sequences. Whether you're testing algorithms or forecasting experimental outcomes, BarcoSim provides a robust framework to mimic real-world sequencing scenarios, ensuring preparedness and enhancing the efficiency of your genomic projects."
https://github.com/loukesio/barcosim
Last synced: 4 days ago
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BarcoSim, a specialized R package designed for simulating barcoded amplicon sequences. Whether you're testing algorithms or forecasting experimental outcomes, BarcoSim provides a robust framework to mimic real-world sequencing scenarios, ensuring preparedness and enhancing the efficiency of your genomic projects."
- Host: GitHub
- URL: https://github.com/loukesio/barcosim
- Owner: loukesio
- License: other
- Created: 2023-04-15T19:24:30.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-12-09T12:31:06.000Z (16 days ago)
- Last Synced: 2024-12-09T13:34:29.043Z (16 days ago)
- Language: R
- Homepage:
- Size: 2.1 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://opensource.org/licenses/MIT)
[](https://github.com/loukesio/barcosim/commits/main)
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[](https://codecov.io/gh/loukesio/barcosim?branch=main)
[](https://www.tidyverse.org/lifecycle/#experimental)
## Install the BarcoSim package
Install the package using the following commands 
```r
# for now you can install the developemental version of ltc
# first you need to install the devtools package
# in case you have not already installed
install.packages("devtools")
# and load it
library(devtools)
# then you can install the dev version of the ltc
devtools::install_github("loukesio/BarcoSim")
# and load it
library(BarcoSim)
```
### 1. Use the `gpseq` command to generate the parent sequences.
Parameters:
- `num_sequences`: An integer specifying the number of DNA sequences to generate.
- `seq_length`: An integer representing the length of each DNA sequence.
- `range_start`: An integer indicating the start position of the barcoded sequence.
- `range_end`: An integer indicating the end position of the barcoded sequence.
``` r
library(Biostrings) # Provides tools for working with biological sequences, such as DNA, RNA, and protein sequences
library(BarcoSim) # BarcoSim: A package for simulating barcoded sequencing data
library(dplyr) # A powerful package for data manipulation and transformation,
set.seed(123) # sets the random seed to ensure the reproducibility of a random processes (generation of sequences)
# This function creates 5 parent sequences, each with 10 base pairs and a single barcode area spanning from base 3 to base 6.
df1.1 <- gpseq(num_sequences=5, seq_length=10, range_start=3, range_end=6)
df1.1 %>%
DNAStringSet()
#> DNAStringSet object of length 10:
#> width seq
#> [1] 10 CGCAGCGTAA
#> [2] 10 CGTGTTGTAA
#> [3] 10 CGGCAAGTAA
#> [4] 10 CGTCGGGTAA
#> [5] 10 CGATGCGTAA
# Create five parent sequences, each consisting of 10 base pairs, with multiple barcoded regions spanning from base 2 to base 3 and
# from base 6 to base 8.
df1.2 <- gpseq(5,10,range_start=c(2,6), range_end=c(3,8))
df1.2 %>%
DNAStringSet()
DNAStringSet object of length 5:
width seq
[1] 10 GCTTAGGACG
[2] 10 GTGTATGGCG
[3] 10 GCGTACTCCG
[4] 10 GGGTATGTCG
[5] 10 GATTAGCTCG
```
Created on 2023-04-15 with [reprex v2.0.2](https://reprex.tidyverse.org)
The outcome of the gpseq contains the conserved sequences from 1-2 and 7-10, and the barcode sequences from 3-6 (see Figure1). In addition with the help of the function `calcSeqSim` we can quantify the similarity among sequences at each base pair.
### 2. Use the `calcSeqSim` function to plot sequence similarity across the parent sequences
parameters:
- `dna_seq`: A character vector of DNA sequences obtained as the output of the `gpseq` function.
Plotting sequence similarity in a sequence with a single barcoded area:
``` r
library(BarcoSim)
library(ggplot2)
library(dplyr)
df1.1 = c("CGCAGCGTAA", "CGTGTTGTAA", "CGGCAAGTAA", "CGTCGGGTAA", "CGATGCGTAA")
df1.1
#> [1] "CGCAGCGTAA" "CGTGTTGTAA" "CGGCAAGTAA" "CGTCGGGTAA" "CGATGCGTAA"
#______________________________________________
# Find sequence similarity at each position
#______________________________________________
calSeqSim(df1.1)
#> [1] 100 100 40 40 60 40 100 100 100 100
#___________________________
# plotting example :)
#____________________________
# Create the tibble
df1.1_data <- calSeqSim(df1.1) %>%
tibble() %>%
dplyr::rename(similarity=1)
# Create the geom area plot
ggplot(df1.1_data, aes(x = 1:nrow(df1.1_data), y = similarity, fill = similarity)) +
geom_area(color = "#333333", fill = "#edae49") +
xlab("Base pair (bp)") +
ylab("Percentage of Similarity") +
ggtitle("Sequnce similarity plot per bp") +
scale_x_continuous(breaks=seq(1:10)) +
theme(panel.grid = element_blank(),
panel.background = element_rect(fill = "white"),
plot.title = element_text(hjust=0.5),
axis.text = element_text(size=12),
axis.ticks.length = unit(.2, "cm")) +
geom_vline(xintercept =c(3,6), linetype="dashed")
# similarly you can plot the df1.2 data
```
### 3. Use the `r_gpseq` command to replicate parent sequences and make a barcode data set.
Parameters:
- `dna_seq`: A character vector of DNA sequences, obtained as the output of the `gpseq` function.
- `num_replicates`: An integer specifying the number of times each parent sequence should be replicated.
- `error_rate`: A numeric value representing the probability error rate during the replication process.
``` r
library(BarcoSim)
print(df1.1)
#> [1] "CGCAGCGTAA" "CGTGTTGTAA" "CGGCAAGTAA" "CGTCGGGTAA" "CGATGCGTAA"
#With the current parameters of the r_gpseq function, you can replicate each parent DNA sequence in dna_seq twice with a 0.1 probability error rate.
r_gpseq(dna_seq=df1.1,num_replicates=2,error_rate=0.1)
#> parent parent_seq offspring
#> 1 1 CGCAGCGTAA CGGTGCGTAA
#> 2 1 CGCAGCGTAA CGCAGCGTAA
#> 3 2 CGTGTTGTAA CGTGTTGTAC
#> 4 2 CGTGTTGTAA CGTGTTGTAA
#> 5 3 CGGCAAGTAA CGGCAAGTAA
#> 6 3 CGGCAAGTAA CCGCAAGTAA
#> 7 4 CGTCGGGTAA CGTCGGGTAC
#> 8 4 CGTCGGGTAA GTCGGGTAA
#> 9 5 CGATGCGTAA GATGCGTAA
#> 10 5 CGATGCGTAA CCATGCGTAA
```
Created on 2023-06-24 with [reprex v2.0.2](https://reprex.tidyverse.org)
### 4. `r_gpseq_csub` replicates parent sequences with a specified error rate while allowing the specification of substitution rates for each base. It is an extension of the r_gpseq function.
- `dna_seq`: A character vector of DNA sequences, obtained as the output of the `gpseq` function.
- `num_replicates`: An integer specifying the number of times each parent sequence should be replicated.
- `error_rate` A numeric value between 0 and 1 representing the probability error rate during the replication process.
- `substitution_probs` (list of length 5): Includes substitution probabilities for each base (A, C, G, T, and empty string).
``` r
library(BarcoSim)
df1.1 = c("GCTTAGGACG", "GTGTATGGCG", "GCGTACTCCG", "GGGTATGTCG", "GATTAGCTCG")
substitution_probs <- list("A" = 0.1, "C" = 0.2, "G" = 0.3, "T" = 0.4, " " = 0.1)
r_gpseq_csub(dna_seq=df1.1,num_replicates=2,error_rate = 0.1, substitution_probs)
#> parent parent_seq offspring
#> 1 1 GCTTAGGACG GCTT AGACG
#> 2 1 GCTTAGGACG GCTTACGACG
#> 3 2 GTGTATGGCG GTGTAGGGCG
#> 4 2 GTGTATGGCG GTGTATAGCG
#> 5 3 GCGTACTCCG GCGTGCTCCG
#> 6 3 GCGTACTCCG GCGTACGCCG
#> 7 4 GGGTATGTCG GGGTATGTCG
#> 8 4 GGGTATGTCG GGGTATGTCG
#> 9 5 GATTAGCTCG GGTTGGCTCG
#> 10 5 GATTAGCTCG GAT GGC CG
```
Created on 2023-06-24 with [reprex v2.0.2](https://reprex.tidyverse.org)