Fast genome analysis from unassembled short reads
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README.md

GenomeScope: Fast genome analysis from unassembled short reads

Vurture, GW, Sedlazeck, FJ, Nattestad, M, Underwood, CJ, Fang, H, Gurtowski, J, Schatz, MC (2017) Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btx153

Current developments in de novo assembly technologies have been focused on relatively simple genomes. Even the human genome, with a heterozygosity rate of only ~0.1% and 2n diploid structure, is significantly simpler than many other species, especially plants. However, genomics is rapidly advancing towards sequencing more complex species such as pineapple, sugarcane, or wheat that have much higher rates of heterozygosity (>1% for pineapple), much higher ploidy (8n for sugarcane), and much larger genomes (16Gbp for wheat).

One of the first goals when sequencing a new species is determining the overall characteristics of the genome structure, including the genome size, abundance of repetitive elements, and the rate of heterozygosity. These features are needed to study trends in genome evolution, and can inform the parameters that should be used for the individual assembly steps. They can also serve as an independent quality control during any analysis, such as quantifying the quality of an assembly, or measuring the expected number of heterozygous bases in the genome before mapping any variants.

We have developed an analytical model and open-source software package GenomeScope that can infer the global properties of a genome from unassembled sequenced data. GenomeScope uses the k-mer count distribution, e.g. from Jellyfish, and within seconds produces a report and several informative plots describing the genome properties. We validate the approach on simulated heterozygous genomes, as well as synthetic crosses of related strains of microbial and eukaryotic genomes with known reference genomes. GenomeScope was also applied to study the characteristics of several novel species, including pineapple, pear, the regenerative flatworm Macrostomum lignano, and the Asian sea bass.

Getting Started

Before running GenomeScope, you must first compute the histogram of k-mer frequencies. We recommend the tool jellyfish that is available here: http://www.genome.umd.edu/jellyfish.html. After compiling jellyfish, you can run it like this:

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

Note you should adjust the memory (-s) and threads (-t) parameter according to your server. This example will use 10 threads and 1GB of RAM. The kmer length (-m) may need to be scaled if you have low coverage or a high error rate. We recommend using a kmer length of 21 (m=21) for most genomes, as this length is sufficiently long that most k-mers are not repetitive and is short enough that the analysis will be more robust to sequencing errors. Extremely large (haploid size >>10GB) and/or very repetitive genomes may benefit from larger kmer lengths to increase the number of unique k-mers. Accurate inferences requires a minimum amount of coverage, at least 25x coverage of the haploid genome or greater, otherwise the model fit will be poor or not converge. GenomeScope also requires relatively low error rate sequencing, such as Illumina sequencing, so that most k-mers do not have errors in them. For example, a 2% error corresponds to an error every 50bp on average, which is greater than the typical k-mer size used (k=21). Notably, raw single molecule sequencing reads from Oxford Nanopore or Pacific Biosciences, which currently average 5-15% error, are not supported as an error will occur on average every 6 to 20 bp. You should always use "canonical kmers" (-C) since the sequencing reads will come from both the forward and reverse strand of DNA.

Then export the kmer count histogram

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

Again the thread count (-t) should be scaled according to your server. After you have the jellyfish histogram file, you can run GenomeScope within the online web tool, or at the command line.

Running GenomeScope Online

Users may prefer to use the online version, which offers all of the same functionality within an easy to use web interface: http://genomescope.org/

Running GenomeScope on the Command Line

Command line users can run the modeling with the R script genomescope.R, making sure that Rscript is in your PATH (alternatively, edit the shebang line to point to the Rscript location)

$ Rscript genomescope.R histogram_file k-mer_length read_length output_dir [kmer_max] [verbose]

The histogram_file (from jellyfish), k-mer_length, read_length, and output_dir are required parameters. The optional parameter kmer_max specifies the cutoff for excluding high frequency kmers from the analysis. We recommend setting kmer_max=1000, but it depends on the specific characteristics of your data. If the optional parameter verbose is set to 1, then GenomeScope will output more details on the model fitting as different parameters are used. The output plots and a text file of the inferred genome characteristics will be output to the specified output_dir directory.

For example, you can download the histogram from the Arabidopsis F1 described in the manuscript here: https://raw.githubusercontent.com/schatzlab/genomescope/master/analysis/real_data/ara_F1_21.hist

Then run GenomeScope like this:

$ /PATH/TO/Rscript /PATH/TO/genomescope.R ara_F1_21.hist 21 150 output

This should complete in less than 1 minute, and report:

Model converged het:0.0104 kcov:22.2 err:0.0035 model fit:0.446 len:151975724

The plots and the full results will be in output directory, showing the estimated genome size to be 151.9Mbp and a 1.04% heterozygosity rate (the exact values may slightly differ due to the randomization within the modeling)

Tutorial

A tutorial by Andrew Severin on running GenomeScope is available here http://gif.biotech.iastate.edu/genomescope

Frequently Asked Questions (FAQ)

> Q: Why didnt the model converge, or why does it give very different results than expected?

A: The most common problem is you have too low of coverage for the model to confidently identify the peaks corresponding to the homozygous kmers. This can be recognized by a lack of any peaks in the kmer plots or that the model fit doesnt match the observed kmer profile very well. To correct this problem, first make sure that you have used the cannonically kmer counting mode (-C if you are using jellyfish). If this still fails, you can try slightly decreasing the kmer size used to 17 or 19. If all of these attempts still fail you will unfortunately need to generate additional sequencing data.

> Q: As mentioned in the Supplementary Notes and Figures 1.3.2 Genome Size Estimation, the haploid genome size is estimated by: "This estimate is revised by summing the total number of k-mers, except presumptive sequencing errors identified as in section 1.3.1, and dividing by the 2*λ, the estimated coverage for homozygous k-mers". If I understand it correctly, λ is the mean of a distribution, the estimated coverage for homozygous k-mers; and in the genomescope profile, kcov is the estimated coverage for heterozygous kmers. Could you explain how genomescope estimates haploid genome size, specifically why dividing by 2 times of the estimated coverage for homozygous k-mers?

A: Thank you for writing. I think there is a bit of confusion over the variable names and how they relate to each other. The first thing to note is λ and kcov refer to the same value, just that we use λ in the written document and kcov in the code. The modeling tries to identify 4 peaks centered at λ, 2λ, 3λ, and 4λ. These 4 peaks correspond to the mean coverage levels of the unique heterozygous, unique homozygous, repetitive heterozygous and repetitive homozygous sequences, respectively. So when it estimates the haploid genome size, it divides by the 2λ, which is the average homozygous coverage, not "2 times the estimated coverage for homozygous k-mers" as you write.

The other potentially confusing aspect is what is meant by haploid genome size versus diploid genome size. We consider the haploid genome size to mean the span of one complete set of haploid chromosomes and the diploid genome size to be the span of both haploid copies (total DNA content in one diploid cell). In particular, in a human cell, the haploid genome size is about 3Gbp and the diploid genome size is about 6Gbp. If you sequence a total of 300Gbp for a human genome, that would be about 150Gbp (50x coverage) of the maternal haplotype and about 150Gbp (50x coverage) of the paternal haplotype. But since the heterozygosity rate in humans is so low, the main peak in the distribution would be centered around 100x. However, GenomeScope will still try to fit the 4 peaks, so should set the heterozygous kmer coverage λ equal to 50x, and thus the homozygous coverage to 2*λ = 100x. From this GenomeScope will compute the haploid genome size as the total amount of sequence data (300GB) divided by the homozygous coverage (100x) to report 3Gbp as expected. Kmers with higher coverage are naturally scaled as well: kmers that occur 200 or 300 times in the kmer profile (and thus are 2 or 3 copy repeats in the diploid genome, 4 or 6 times in the haploid sequences) are still scaled by 100x to contribute 2 or 3 copies to the estimate. Finally, note that if the two haplotypes have significantly different lengths, then the reported haploid genome size will be the average of the two.

> Q: Can GenomeScope be used to estimate ploidy, or used with genomes with higher ploidy?

A: No, GenomeScope is only appropriate for diploid genomes. In principle the model could be extend to higher levels of polyploidy by extending the model to consider additional peaks in the k-mer profile, but this is not currently supported. GenomeScope also does not support genomes that have uneven copy number of their chromosomes, such as aneuploid cancer genomes or even unequal numbers of sex chromosomes. In these scenarios the reported heterozygosity rate will represent the fraction of bases that are haploid (copy number 1) versus diploid (copy number 2) as well as any heterozygous positions in the other chromosomes.

> Q: I tried out GenomeScope in order to obtain a genome size estimate for an organism that I am working on. Using the widely-used and cited k-mer method and calculation outlined in the XXX paper, I got an estimate of 869 - 919 Mbp and this is somewhat consistent with a c-value of 0.83pg from a different published study. However, with GenomeScope, I got an estimate of 650 Mbp instead. Would you or your team have any insights into why I am observing this discrepancy of more than 200Mbp in my estimations?

While GenomeScope can automate most of the analysis, it does have one critical parameter on which high frequency kmers should be filtered out. This parameter is needed because we often see in real samples that kmers that occur 10,000 times or 100,000 times or greater are artifacts such as phiX sequencing, or organelle sequencing (or other contamination). To account for these, GenomeScope will by default exclude any kmers that occur more than 1000 times from the analysis, which lead to a genome size estimate of 649Mbp. If you increase this cutoff to 10,000, then the new size estimate is 697Mbp. You could perhaps raise this limit even higher, but it looks like your histogram is truncated at 10,000 (which is the default for jellyfish). If you want to include these ultrahigh frequency kmers, then you will have to regenerate the histogram from jellyfish and then set the max coverage threshold to 100,000 or perhaps even 1,000,000. This will likely increase the estimated genome size, but also make the analysis even more sensitive to any artifacts in the data. Unfortunately every project is a little bit different on how to best remove those artifacts. Please see the paper for details (especially the section in the supplement on characterizing the high frequency kmers in Arabidopsis)

> Q: I sequenced the gDNA of two closely related fish samples, and GenomeScope reports the heterozygosity rate of each separately at 0.103% and 0.113%. However, when I merge the reads together, GenomeScope reports an overall rate of heterozygosity to be lower at 0.056%. Why is that?

The short answer is by mixing the samples together, this becomes a tetraploid sample, but GenomeScope currently doesnt work with ploidy > 2. Ive been doing some simulations to further understand this: I randomly generate a 1Mbp maternal sequence m1, and then introduce heterozygous variants to create the paternal sequence p1 at a given rate of heterozygosity r1. In parallel, I create a second maternal genome m2 that differs from m1 by a separate rate of heterozygosity rM. From m2, I derive the paternal genome p2 using the rate of heterozygosity r2. Note that there are 3 rates of heterozygosity that can be adjusted (r1, r2, and rM), and from your data we know that r1 and r2 are around 0.1% but rM is unknown, although is assumed to be very low because the mitochondrial genomes are identical. From this framework, I tried several values of rM, and see that when rM is set to 0.02% then GenomeScope infers the overall rate of heterozygosity at about 0.05%, similar to your data (see attached results). In the joint GenomeScope plot, there is a new peak of heterozygous kmers centered at around 10x coverage (below the expected coverage for heterozygous variants), but GenomeScope incorrectly assumes these are errors just because it doesnt understand how to deal with higher levels of ploidy. We are working on extended the model to consider situations like this, but for now if you want to demonstrate this further, you'd have to align the reads to your assembly, and then you should detect variants that occur at about 50% allele frequency (where m1 and m2 are different), plus variants that occur at about 25% allele frequency (where there is further heterozygosity in p1 or p2). If you would like to run additional simulations, the code is available in the repo at https://github.com/schatzlab/genomescope/tree/master/analysis/genomesim/polyploid

> Q: Can you please define the terms on the plot:

The published paper, and especially the supplemental methods defines the terms more completely but briefly:

len: inferred total genome length
uniq: percent of the genome that is unique (not repetitive)
het: overall rate of heterozygosity
kcov: mean kmer coverage for heterozygous bases. note the top of the peak will not intersect the kcov line because of the over dispersion in real data
err: error rate of the reads <br< dup: average rate of read duplications

Resources

VCF files of the variants identified in the larger genomes are available here: http://labshare.cshl.edu/shares/schatzlab/www-data/genomescope/vcf/

References:

Vurture, GW, Sedlazeck, FJ, Nattestad, M, Underwood, CJ, Fang, H, Gurtowski, J, Schatz, MC (2017) Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btx153