GenomeScope 2.0

http://genomescope.org/
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Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based...
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### List FASTQ files for KMC

Source: http://genomescope.org/genomescope2

Create a file containing a list of all FASTQ files to be processed by KMC.

```bash
$ ls *.fastq > FILES
```

--------------------------------

### Create temporary directory for KMC

Source: http://genomescope.org/genomescope2

Create a temporary directory required for KMC processing.

```bash
mkdir tmp
```

--------------------------------

### Count k-mers with Jellyfish

Source: http://genomescope.org/genomescope2

Use Jellyfish to count k-mers from FASTQ files. Adjust memory (-s) and threads (-t) based on your server. Always use canonical k-mers (-C).

```bash
$ jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf
```

--------------------------------

### Export k-mer histogram with Jellyfish

Source: http://genomescope.org/genomescope2

Export the k-mer count histogram from Jellyfish output. Scale thread count (-t) according to your server.

```bash
$ jellyfish histo -t 10 reads.jf > reads.histo
```

--------------------------------

### GenomeScope 2.0 Model Parameters

Source: http://genomescope.org/genomescope2/analysis.php?code=example11

Presents the fitted model formula and estimated parameters from a GenomeScope 2.0 analysis. This includes coefficients for various genomic features and convergence statistics. Use this to understand the model's fit to the data.

```text
Formula: y_transform ~ x^transform_exp * length * predict6_0(r1, 
    r2, r3, r4, r5, r6, r7, r8, r9, r10, k, d, kmercov, bias, 
    x)

Parameters:
         Estimate Std. Error   t value Pr(>|t|)    
d       6.239e-01  1.557e-03   400.795   <2e-16 ***
r1      1.000e-05  3.438e-04     0.029    0.977    
r2      3.311e-03  1.531e+01     0.000    1.000    
r3      1.889e-02  8.856e-05   213.258   <2e-16 ***
r4      7.698e-04  1.531e+01     0.000    1.000    
r5      2.727e-02  1.753e-01     0.156    0.876    
r6      2.522e-02  2.124e+01     0.001    0.999    
r7      1.000e-05  1.752e-01     0.000    1.000    
r8      2.199e-03  3.576e+01     0.000    1.000    
r9      1.440e-03  1.736e+01     0.000    1.000    
r10     2.161e-02  7.262e-05   297.607   <2e-16 ***
kmercov 5.257e+01  1.628e-03 32289.245   <2e-16 ***
bias    8.362e-01  5.696e-04  1467.981   <2e-16 ***
length  5.002e+08  5.022e+05   996.033   <2e-16 ***
--- 
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 2544000 on 999956 degrees of freedom

Number of iterations to convergence: 66 
Achieved convergence tolerance: 1.49e-08


```

--------------------------------

### GenomeScope 2.0 Model Parameters

Source: http://genomescope.org/genomescope2/analysis.php?code=example10

This section details the statistical model used by GenomeScope 2.0, including the formula and estimated parameters with their significance. It is useful for understanding the model's fit and the contribution of different factors to the analysis.

```text
Formula: y_transform ~ x^transform_exp * length * predict4_0(r1, 
    r2, r3, r4, k, d, kmercov, bias, x)

Parameters:
         Estimate Std. Error  t value Pr(>|t|)    
d       1.330e-01  2.903e-04  457.966   <2e-16 ***
r1      4.531e-02  3.134e-05 1445.708   <2e-16 ***
r2      2.173e-02  2.048e-04  106.085   <2e-16 ***
r3      1.000e-05  3.063e-04    0.033    0.974    
r4      2.119e-03  9.728e-05   21.787   <2e-16 ***
kmercov 2.426e+01  4.017e-03 6039.897   <2e-16 ***
bias    1.139e+00  1.393e-03  817.501   <2e-16 ***
length  3.731e+08  1.070e+05 3487.071   <2e-16 ***
--- 
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 424800 on 999971 degrees of freedom

Number of iterations to convergence: 24 
Achieved convergence tolerance: 1.49e-08


```

--------------------------------

### Count k-mers with KMC

Source: http://genomescope.org/genomescope2

Use KMC to count k-mers. Adjust memory (-m) and threads (-t) for your server. The k-mer length (-k) may need scaling for low coverage or high error rates. Bounds (-ci, -cs) exclude k-mers outside specified counts.

```bash
$ kmc -k21 -t10 -m64 -ci1 -cs10000 @FILES reads tmp/
```

--------------------------------

### GenomeScope 2.0 Analysis Progress

Source: http://genomescope.org/genomescope2/analysis.php?code=example10

This log shows the iterative progress of the GenomeScope 2.0 analysis. It details the trimming steps and model fitting at each round, indicating convergence and the score achieved.

```text
starting 
round 0 trimming to 6 trying 2p peak model... converged. score: 198630610233765280 
round 1 trimming to 11 trying 2p peak model... converged. score: 196035062284482592 
round 2 trimming to 16 trying 2p peak model... converged. score: 187940943959353760 
round 3 trimming to 21 trying 2p peak model... converged. score: 177023847393578464 
done 

```

--------------------------------

### GenomeScope Model Parameters

Source: http://genomescope.org/genomescope2/analysis.php?code=example7

Presents the fitted model formula and the estimated parameters, including their standard errors, t-values, and significance codes. This output is crucial for understanding the model's fit and the contribution of each parameter.

```text
Formula: y_transform ~ x^transform_exp * length * predict3_0(r1, 
    r2, k, d, kmercov, bias, x)

Parameters:
         Estimate Std. Error t value Pr(>|t|)    
d       1.354e-01  1.360e-04   995.4   <2e-16 ***
r1      3.355e-02  1.538e-05  2182.5   <2e-16 ***
r2      1.029e-02  5.512e-06  1866.4   <2e-16 ***
kmercov 2.787e+01  3.057e-03  9117.5   <2e-16 ***
bias    1.108e+00  9.652e-04  1147.4   <2e-16 ***
length  4.810e+09  9.411e+05  5110.6   <2e-16 ***
--- 
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 5346000 on 999969 degrees of freedom

Number of iterations to convergence: 6 
Achieved convergence tolerance: 1.49e-08


```

--------------------------------

### GenomeScope 2.0 Progress Log

Source: http://genomescope.org/genomescope2/analysis.php?code=example11

Shows the iterative progress of the GenomeScope 2.0 analysis, indicating trimming steps and model convergence. This log helps in understanding the analysis workflow and potential issues.

```text
starting 
round 0 trimming to 15 trying 2p peak model... converged. score: 6295284274002482176 
round 1 trimming to 20 trying 2p peak model... converged. score: 6293966612129074176 
round 2 trimming to 25 trying 2p peak model... converged. score: 6289477665936505856 
round 3 trimming to 30 trying 2p peak model... converged. score: 6272593770753348608 
done 

```

--------------------------------

### Transform KMC output to histogram

Source: http://genomescope.org/genomescope2

Transform KMC output into a k-mer count histogram. The -cx option sets the cutoff for the histogram.

```bash
$ kmc_tools transform reads histogram reads.histo -cx10000
```

--------------------------------

### GenomeScope 2.0 Analysis Results

Source: http://genomescope.org/genomescope2/analysis.php?code=example8

Displays the output of a GenomeScope 2.0 analysis, including version, parameters, and statistical properties of the genome. This output is generated after running the GenomeScope analysis on a genome dataset.

```text
GenomeScope version 2.0
p = 4
k = 21
initial kmercov estimate = 79
NO_UNIQUE_SEQUENCE set to TRUE

property                      min               max               
Homozygous (aaaa)             88.2864%          88.5444%          
Heterozygous (not aaaa)       11.4556%          11.7136%          
aaab                          0%                0.05526%          
aabb                          5.40059%          5.44174%          
aabc                          0.603173%         0.73443%          
abcd                          5.45188%          5.48219%          
Genome Haploid Length         572,729,399 bp    572,773,156 bp    
Genome Repeat Length          434,169,479 bp    434,202,649 bp    
Genome Unique Length          138,559,920 bp    138,570,507 bp    
Model Fit                     54.6064%          90.0372%          
Read Error Rate               0.196664%         0.196664%         


```

--------------------------------

### GenomeScope 2.0 Analysis Results

Source: http://genomescope.org/genomescope2/analysis.php?code=example10

This output displays the estimated genome properties derived from GenomeScope 2.0 analysis. It includes statistics on homozygous and heterozygous regions, repeat and unique lengths, and model fit.

```text
GenomeScope version 2.0
p = 4
k = 21
initial kmercov estimate = 23
NO_UNIQUE_SEQUENCE set to TRUE

property                      min               max               
Homozygous (aaaa)             92.9548%          93.1504%          
Heterozygous (not aaaa)       6.84956%          7.0452%           
aaab                          4.52507%          4.53761%          
aabb                          2.132%            2.21394%          
aabc                          0%                0.0622612%        
abcd                          0.192484%         0.231395%         
Genome Haploid Length         751,908,823 bp    752,406,949 bp    
Genome Repeat Length          428,529,485 bp    428,813,378 bp    
Genome Unique Length          323,379,338 bp    323,593,571 bp    
Model Fit                     51.8623%          95.3911%          
Read Error Rate               0.308181%         0.308181%         


```

--------------------------------

### GenomeScope Analysis Progress

Source: http://genomescope.org/genomescope2/analysis.php?code=example7

Tracks the iterative progress of the GenomeScope model fitting process, showing the trimming values, model type, convergence status, and scores for each round.

```text
starting 
round 0 trimming to 10 trying 2p peak model... converged. score: 29100840861034582016 
round 1 trimming to 15 trying 2p peak model... converged. score: 29000332708657721344 
round 2 trimming to 20 trying 2p peak model... converged. score: 28781942559245672448 
round 3 trimming to 25 trying 2p peak model... converged. score: 28501936939239657472 
done 

```

--------------------------------

### GenomeScope 2.0 Analysis Results

Source: http://genomescope.org/genomescope2/analysis.php?code=example11

Displays key statistics from a GenomeScope 2.0 analysis, including estimated genome lengths, repeat content, and read error rates. This output is generated after the analysis is complete.

```text
GenomeScope version 2.0
p = 6
k = 21
initial kmercov estimate = 51
NO_UNIQUE_SEQUENCE set to TRUE

property                      min               max               
Homozygous (aaaaaa)           89.9276%
Heterozygous (not aaaaaa)     10.0724%
Genome Haploid Length         2,351,570,838 bp  2,351,862,170 bp  
Genome Repeat Length          2,163,467,601 bp  2,163,735,628 bp  
Genome Unique Length          188,103,238 bp    188,126,541 bp    
Model Fit                     32.179%           90.5483%
Read Error Rate               0.506403%         0.506403%


```
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