### List FASTQ files for KMC Source: http://genomescope.org/genomescope2.0 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/genomescope2.0 Create a temporary directory to store KMC intermediate files. ```bash mkdir tmp ``` -------------------------------- ### Count k-mers with Jellyfish Source: http://genomescope.org/genomescope2.0 Use this command to count canonical k-mers from FASTQ files. Adjust memory (-s) and threads (-t) based on your server resources. 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 Jellyfish k-mer histogram Source: http://genomescope.org/genomescope2.0 Export the k-mer count histogram from Jellyfish output. Scale the thread count (-t) according to your server. ```bash $ jellyfish histo -t 10 reads.jf > reads.histo ``` -------------------------------- ### Genome Analysis Model Parameters Source: http://genomescope.org/genomescope2.0/analysis.php?code=example8 Presents the statistical model formula and estimated parameters with their significance. This output is crucial for understanding the model's fit and the contribution of each parameter 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 4.143e-01 6.258e-04 662.126 <2e-16 *** r1 1.000e-05 2.713e-04 0.037 0.971 r2 5.421e-02 1.029e-04 527.062 <2e-16 *** r3 6.688e-03 3.281e-04 20.381 <2e-16 *** r4 5.467e-02 7.576e-05 721.594 <2e-16 *** kmercov 8.264e+01 1.578e-03 52357.386 <2e-16 *** bias 1.661e+00 5.402e-04 3075.388 <2e-16 *** length 2.366e+08 1.070e+05 2211.405 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 738400 on 999962 degrees of freedom Number of iterations to convergence: 30 Achieved convergence tolerance: 1.49e-08 ``` -------------------------------- ### Genome Analysis Model Formula and Parameters Source: http://genomescope.org/genomescope2.0/analysis.php?code=example6 Presents the mathematical formula and estimated parameters for the genome analysis model. This includes coefficients for different components of the model and their statistical significance. ```r Formula: 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) Parameters: Estimate Std. Error t value Pr(>|t|) d 3.014e-02 2.649e-04 113.8 <2e-16 *** r 1.075e-02 5.319e-06 2021.8 <2e-16 *** kmercov 2.211e+01 1.569e-03 14087.5 <2e-16 *** bias 4.634e-01 8.217e-04 564.0 <2e-16 *** length 1.107e+08 5.573e+04 1987.0 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 3862 on 24728 degrees of freedom Number of iterations to convergence: 6 Achieved convergence tolerance: 2.231e-06 ``` -------------------------------- ### Count k-mers with KMC Source: http://genomescope.org/genomescope2.0 Count k-mers using KMC, specifying k-mer length (-k), threads (-t), memory (-m), and bounds for k-mer counts (-ci, -cs). Adjust parameters based on your server and data characteristics. ```bash kmc -k21 -t10 -m64 -ci1 -cs10000 @FILES reads tmp/ ``` -------------------------------- ### GenomeScope 2.0 Model Parameters Source: http://genomescope.org/genomescope2.0/analysis.php?code=example10 Presents the mathematical formula and estimated parameters for the GenomeScope 2.0 model, including significance codes for each parameter. This output is crucial for understanding the model's fit and the contribution of each variable. ```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 ``` -------------------------------- ### GenomeScope 2.0 Progress Log Source: http://genomescope.org/genomescope2.0/analysis.php?code=example10 Tracks the iterative progress of the GenomeScope 2.0 analysis, showing the rounds of trimming and model fitting. This log is useful for monitoring the analysis process and identifying potential convergence issues. ```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 2.0 Model Parameters Source: http://genomescope.org/genomescope2.0/analysis.php?code=example7 Presents the mathematical formula and estimated parameters for the GenomeScope 2.0 model, including coefficients for 'd', 'r1', 'r2', 'kmercov', 'bias', and 'length', along with their statistical significance. ```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 ``` -------------------------------- ### Export KMC k-mer histogram Source: http://genomescope.org/genomescope2.0 Transform KMC results into a histogram format for GenomeScope. The -cx option sets the cutoff for the histogram. ```bash kmc_tools transform reads histogram reads.histo -cx10000 ``` -------------------------------- ### GenomeScope 2.0 Progress Log Source: http://genomescope.org/genomescope2.0/analysis.php?code=example11 Tracks the iterative progress of the GenomeScope 2.0 model fitting process, showing trimming values and convergence scores for each round. ```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 ``` -------------------------------- ### GenomeScope 2.0 Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example7 Displays the output of the GenomeScope 2.0 analysis, including version information, parameters used, and statistical properties of the genome such as homozygous and heterozygous percentages, and estimated genome lengths. ```text GenomeScope version 2.0 p = 3 k = 31 initial kmercov estimate = 27 NO_UNIQUE_SEQUENCE set to TRUE property min max Homozygous (aaa) 95.6115% 95.6198% Heterozygous (not aaa) 4.38016% 4.38852% aab 3.35241% 3.35856% abc 1.02775% 1.02996% Genome Haploid Length 8,949,767,894 bp 8,953,695,151 bp Genome Repeat Length 4,792,368,862 bp 4,794,471,807 bp Genome Unique Length 4,157,399,031 bp 4,159,223,344 bp Model Fit 56.0498% 96.7787% Read Error Rate 0.285544% 0.285544% ``` -------------------------------- ### GenomeScope Analysis Progress Source: http://genomescope.org/genomescope2.0/analysis.php?code=example7 Tracks the progress of the GenomeScope analysis, showing iterative steps of trimming and model convergence with associated scores. ```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 ``` -------------------------------- ### Genome Analysis Progress Log Source: http://genomescope.org/genomescope2.0/analysis.php?code=example8 Tracks the iterative progress of the GenomeScope analysis, showing trimming steps and model convergence scores. This log helps in understanding the refinement process of the analysis. ```text starting round 0 trimming to 15 trying 2p peak model... converged. score: 532349517611601920 round 1 trimming to 20 trying 2p peak model... converged. score: 532364099932201728 round 2 trimming to 25 trying 2p peak model... converged. score: 532486792683885760 round 3 trimming to 30 trying 2p peak model... converged. score: 532432031845827712 done ``` -------------------------------- ### GenomeScope Analysis Progress Source: http://genomescope.org/genomescope2.0/analysis.php?code=example9 Tracks the iterative process of the GenomeScope analysis, showing the trimming parameters and convergence scores for each round. This helps in monitoring the analysis's refinement stages. ```text starting round 0 trimming to 15 trying 2p peak model... converged. score: 26487003968702944 round 1 trimming to 20 trying 2p peak model... converged. score: 26487003963949460 round 2 trimming to 25 trying 2p peak model... converged. score: 26487003948433368 round 3 trimming to 30 trying 2p peak model... converged. score: 26487003944705224 done ``` -------------------------------- ### GenomeScope Model Formula and Parameters Source: http://genomescope.org/genomescope2.0/analysis.php?code=example5 Presents the mathematical formula and estimated parameters for the GenomeScope model. This includes coefficients, standard errors, and significance levels. The model is used to estimate genomic properties. ```r Formula: 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) Parameters: Estimate Std. Error t value Pr(>|t|) d 9.753e-03 2.985e-04 32.68 <2e-16 *** r 6.462e-03 6.201e-06 1042.15 <2e-16 *** kmercov 2.073e+01 2.283e-03 9081.45 <2e-16 *** bias 1.525e+00 2.137e-03 713.92 <2e-16 *** length 1.191e+08 6.338e+04 1879.18 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 4093 on 13622 degrees of freedom Number of iterations to convergence: 8 Achieved convergence tolerance: 4.568e-06 ``` -------------------------------- ### GenomeScope 2.0 Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example10 Displays the statistical breakdown of genome properties, including homozygous and heterozygous percentages, and estimated lengths of different genome components. This output is generated after the primary analysis is complete. ```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% ``` -------------------------------- ### Genome Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example3 Displays key metrics from a genome analysis, including heterozygosity, genome lengths, and read duplication levels. This output is typically generated after running a genome analysis tool. ```text k = 21 property min max Heterozygosity 1.68553% 1.68874% Genome Haploid Length 753,296,002 bp 753,588,757 bp Genome Repeat Length 507,575,498 bp 507,772,758 bp Genome Unique Length 245,720,504 bp 245,815,999 bp Read Duplication Level 1.759X 1.765X Read Error Rate 0.348319% 0.348319% Model Score = 215.572051511197 ``` -------------------------------- ### GenomeScope 2.0 Wheat Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example11 Displays the statistical summary of the GenomeScope 2.0 analysis for wheat, including estimates for homozygous and heterozygous content, genome lengths, and read error rate. ```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% ``` -------------------------------- ### Genome Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example1 Displays key metrics from genome analysis, such as heterozygosity, genome length, repeat length, unique length, duplication level, and error rate. This output is typically generated after running an analysis tool. ```text k = 21 property min max Heterozygosity 0.471783% 0.473875% Genome Haploid Length 564,146,313 bp 564,336,784 bp Genome Repeat Length 27,775,552 bp 27,784,930 bp Genome Unique Length 536,370,761 bp 536,551,855 bp Read Duplication Level 2.556X 2.566X Read Error Rate 0.242698% 0.242698% Model Score = 1.80220241295412 ``` -------------------------------- ### Genome Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example5 Displays statistical properties of the genome, such as heterozygosity, length, and duplication levels. This output is generated after the analysis is complete. ```text k = 21 property min max Heterozygosity 0.645581% 0.646821% Genome Haploid Length 142,555,034 bp 142,586,433 bp Genome Repeat Length 25,630,339 bp 25,635,984 bp Genome Unique Length 116,924,696 bp 116,950,449 bp Read Duplication Level 1.523X 1.527X Read Error Rate 0.156334% 0.156334% Model Score = 359.141543956541 ``` -------------------------------- ### Genome Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example6 Displays key statistics derived from genome analysis, such as heterozygosity, genome length, repeat content, and read duplication levels. These metrics are crucial for understanding genome characteristics. ```text k = 21 property min max Heterozygosity 1.07489% 1.07595% Genome Haploid Length 152,706,039 bp 152,727,721 bp Genome Repeat Length 47,837,766 bp 47,844,558 bp Genome Unique Length 104,868,274 bp 104,883,163 bp Read Duplication Level 0.4626X 0.4642X Read Error Rate 0.336968% 0.336968% Model Score = 892.664111717184 ``` -------------------------------- ### Cotton Genome Analysis Results Source: http://genomescope.org/genomescope2.0/analysis.php?code=example8 Displays key statistics and estimations from the GenomeScope analysis, including homozygous and heterozygous percentages, genome lengths, and read error rate. This output is generated after the analysis is complete. ```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% ``` -------------------------------- ### Genome Analysis Statistical Model Source: http://genomescope.org/genomescope2.0/analysis.php?code=example3 Presents the formula and estimated parameters for a statistical model used in genome analysis. This includes coefficients, standard errors, and significance levels. The model is used to interpret genomic data. ```r Formula: 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) Parameters: Estimate Std. Error t value Pr(>|t|) d 1.831e-01 3.922e-04 466.9 <2e-16 *** r 1.687e-02 1.604e-05 1051.6 <2e-16 *** kmercov 4.236e+01 8.229e-03 5147.3 <2e-16 *** bias 1.762e+00 3.424e-03 514.6 <2e-16 *** length 3.486e+08 3.225e+05 1080.8 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 16360 on 87228 degrees of freedom Number of iterations to convergence: 8 Achieved convergence tolerance: 3.583e-06 ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.