De novo sequence assemblers

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De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers.

Contents

Types of de novo assemblers

There are two types of algorithms that are commonly utilized by these assemblers: greedy, which aim for local optima, and graph method algorithms, which aim for global optima. Different assemblers are tailored for particular needs, such as the assembly of (small) bacterial genomes, (large) eukaryotic genomes, or transcriptomes.

Greedy algorithm assemblers are assemblers that find local optima in alignments of smaller reads. Greedy algorithm assemblers typically feature several steps: 1) pairwise distance calculation of reads, 2) clustering of reads with greatest overlap, 3) assembly of overlapping reads into larger contigs, and 4) repeat. These algorithms typically do not work well for larger read sets, as they do not easily reach a global optimum in the assembly, and do not perform well on read sets that contain repeat regions. [1] Early de novo sequence assemblers, such as SEQAID [2] (1984) and CAP [3] (1992), used greedy algorithms, such as overlap-layout-consensus (OLC) algorithms. These algorithms find overlap between all reads, use the overlap to determine a layout (or tiling) of the reads, and then produce a consensus sequence. Some programs that used OLC algorithms featured filtration (to remove read pairs that will not overlap) and heuristic methods to increase speed of the analyses.

Graph method assemblers [4] come in two varieties: string and De Bruijn. String graph and De Bruijn graph method assemblers were introduced at a DIMACS [5] workshop in 1994 by Waterman [6] and Gene Myers. [7] These methods represented an important step forward in sequence assembly, as they both use algorithms to reach a global optimum instead of a local optimum. While both of these methods made progress towards better assemblies, the De Bruijn graph method has become the most popular in the age of next-generation sequencing. During the assembly of the De Bruijn graph, reads are broken into smaller fragments of a specified size, k. The k-mers are then used as edges in the graph assembly. Nodes are built as (k-1)-mers connect by an edge. The assembler will then construct sequences based on the De Bruijn graph. De Bruijn graph assemblers typically perform better on larger read sets than greedy algorithm assemblers (especially when they contain repeat regions).

Commonly used programs

List of de-novo assemblers
NameDescription /

Methodology

TechnologiesAuthorPresented /

Last updated

Licence*Homepage
ABySSparallel, paired-end sequence assembler designed for large genome assembly of short reads (genomic and transcriptomic), employ a Bloom filter to De Bruijn graphIllumina [8] [9] 2009 / 2017OS link
DISCOVARpaired-end PCR-free reads (successor of ALLPATHS-LG)Illumina (MiSeq or HiSeq 2500) [10] 2014OS link
DNA Baser Sequence AssemblerDNA sequence assembly with automatic end trimming & ambiguity correction. Includes a base caller.Sanger, IlluminaHeracle BioSoft SRL2018.09C ($69)NA
DNASTAR Lasergene GenomicsLarge genomes, exomes, transcriptomes, metagenomes, ESTs. Also de novo assembly and polishing of long read sequencing data from Oxford Nanopore and PacBio, including PacBio Hifi reads.Illumina, ABI SOLiD, Roche 454, Ion Torrent, Solexa, Sanger DNASTAR 2007 / 2023C link
Flyegenomes and metagenomes. Makes use of repeat graphsPacBio/Oxford Nanopore reads [11] 2018/2023OS link
Newbler genomes, ESTs454, Sanger 454 Life Sciences 2004/2012C link
Phrap genomesSanger, 454, Solexa Green, P. 1994 / 2008C / NC-A link
PlassProtein-level assembler: assembles six-frame-translated sequencing reads into protein sequencesIllumina [12] 2018 / 2019OS link
Raya suite of assemblers including de novo, metagenomic, ontology and taxonomic profiling; uses a De Bruijn graph [13] 2010OS link
SPAdes (small) genomes, single-cellIllumina, Solexa, Sanger, 454, Ion Torrent, PacBio, Oxford Nanopore [14] 2012 / 2021OS link
Velvet (small) genomesSanger, 454, Solexa, SOLiD [15] 2007 / 2011OS link
HGAPGenomes up to 130 MBPacBio reads [16] 2011 / 2015OS link
FalconDiploid genomesPacBio reads [17] 2014 / 2017OS link
CanuSmall and large, haploid/diploid genomesPacBio/Oxford Nanopore reads [18] 2001 / 2018OS link
MaSuRCAAny size, haploid/diploid genomesIllumina and PacBio/Oxford Nanopore data, legacy 454 and Sanger data [19] 2011 / 2018OS link
HingeSmall microbial genomesPacBio/Oxford Nanopore reads [20] 2016 / 2018OS link
Trinitytranscriptome assemblies by de Bruijn graphIllumina RNA-seq [21] 2011 link
*Licences: OS = Open Source; C = Commercial; C / NC-A = Commercial but free for non-commercial and academics

Different assemblers are designed for different type of read technologies. Reads from second generation technologies (called short read technologies) like Illumina are typically short (with lengths of the order of 50-200 base pairs) and have error rates of around 0.5-2%, with the errors chiefly being substitution errors. However, reads from third generation technologies like PacBio and fourth generation technologies like Oxford Nanopore (called long read technologies) are longer with read lengths typically in the thousands or tens of thousands and have much higher error rates of around 10-20% with errors being chiefly insertions and deletions. This necessitates different algorithms for assembly from short and long read technologies.

Assemblathon

There are numerous programs for de novo sequence assembly and many have been compared in the Assemblathon. The Assemblathon is a periodic, collaborative effort to test and improve the numerous assemblers available. Thus far, two assemblathons have been completed (2011 and 2013) and a third is in progress (as of April 2017). Teams of researchers from across the world choose a program and assemble simulated genomes (Assemblathon 1) and the genomes of model organisms whose that have been previously assembled and annotated (Assemblathon 2). The assemblies are then compared and evaluated using numerous metrics.

Assemblathon 1

Assemblathon 1 [22] was conducted in 2011 and featured 59 assemblies from 17 different groups and the organizers. The goal of this Assembalthon was to most accurately and completely assemble a genome that consisted of two haplotypes (each with three chromosomes of 76.3, 18.5, and 17.7 Mb, respectively) that was generated using Evolver. Numerous metrics were used to assess the assemblies, including: NG50 (point at which 50% of the total genome size is reached when scaffold lengths are summed from the longest to the shortest), LG50 (number of scaffolds that are greater than, or equal to, the N50 length), genome coverage, and substitution error rate.

Assemblathon 2

Assemblathon 2 [23] improved on Assemblathon 1 by incorporating the genomes of multiples vertebrates (a bird (Melopsittacus undulatus), a fish (Maylandia zebra), and a snake (Boa constrictor constrictor)) with genomes estimated to be 1.2, 1.0, and 1.6Gbp in length) and assessment by over 100 metrics. Each team was given four months to assemble their genome from Next-Generation Sequence (NGS) data, including Illumina and Roche 454 sequence data.

See also

Related Research Articles

In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript (ESTs).

In graph theory, an n-dimensional De Bruijn graph of m symbols is a directed graph representing overlaps between sequences of symbols. It has mn vertices, consisting of all possible length-n sequences of the given symbols; the same symbol may appear multiple times in a sequence. For a set of m symbols S = {s1, …, sm}, the set of vertices is:

<span class="mw-page-title-main">Phred quality score</span> Measurement in DNA sequencing

A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. It was originally developed for the computer program Phred to help in the automation of DNA sequencing in the Human Genome Project. Phred quality scores are assigned to each nucleotide base call in automated sequencer traces. The FASTQ format encodes phred scores as ASCII characters alongside the read sequences. Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences.

<i>k</i>-mer Substrings of length k contained in a biological sequence

In bioinformatics, k-mers are substrings of length contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides, k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term k-mer refers to all of a sequence's subsequences of length , such that the sequence AGAT would have four monomers, three 2-mers, two 3-mers and one 4-mer (AGAT). More generally, a sequence of length will have k-mers and total possible k-mers, where is number of possible monomers.

Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of errors and the simplification of repeated regions. Velvet has also been implemented in commercial packages, such as Sequencher, Geneious, MacVector and BioNumerics.

<span class="mw-page-title-main">RNA-Seq</span> Lab technique in cellular biology

RNA-Seq is a technique that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.

SOAP is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.

<span class="mw-page-title-main">Hybrid genome assembly</span>

In bioinformatics, hybrid genome assembly refers to utilizing various sequencing technologies to achieve the task of assembling a genome from fragmented, sequenced DNA resulting from shotgun sequencing. Genome assembly presents one of the most challenging tasks in genome sequencing as most modern DNA sequencing technologies can only produce reads that are, on average, 25-300 base pairs in length. This is orders of magnitude smaller than the average size of a genome. This assembly is computationally difficult and has some inherent challenges, one of these challenges being that genomes often contain complex tandem repeats of sequences that can be thousands of base pairs in length. These repeats can be long enough that second generation sequencing reads are not long enough to bridge the repeat, and, as such, determining the location of each repeat in the genome can be difficult. Resolving these tandem repeats can be accomplished by utilizing long third generation sequencing reads, such as those obtained using the PacBio RS DNA sequencer. These sequences are, on average, 10,000-15,000 base pairs in length and are long enough to span most repeated regions. Using a hybrid approach to this process can increase the fidelity of assembling tandem repeats by being able to accurately place them along a linear scaffold and make the process more computationally efficient.

De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome.

In DNA sequencing, a read is an inferred sequence of base pairs corresponding to all or part of a single DNA fragment. A typical sequencing experiment involves fragmentation of the genome into millions of molecules, which are size-selected and ligated to adapters. The set of fragments is referred to as a sequencing library, which is sequenced to produce a set of reads.

<span class="mw-page-title-main">Scaffolding (bioinformatics)</span> Bioinformatics technique

Scaffolding is a technique used in bioinformatics. It is defined as follows:

Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically contiguous sequences corresponding to read overlaps.

SPAdes is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. Therefore, it might not be suitable for large genomes projects.

In bioinformatics, a DNA read error occurs when a sequence assembler changes one DNA base for a different base. The reads from the sequence assembler can then be used to create a de Bruijn graph, which can be used in various ways to find errors.

In genetics, coverage is one of several measures of the depth or completeness of DNA sequencing, and is more specifically expressed in any of the following terms:

In molecular phylogenetics, relationships among individuals are determined using character traits, such as DNA, RNA or protein, which may be obtained using a variety of sequencing technologies. High-throughput next-generation sequencing has become a popular technique in transcriptomics, which represent a snapshot of gene expression. In eukaryotes, making phylogenetic inferences using RNA is complicated by alternative splicing, which produces multiple transcripts from a single gene. As such, a variety of approaches may be used to improve phylogenetic inference using transcriptomic data obtained from RNA-Seq and processed using computational phylogenetics.

Third-generation sequencing is a class of DNA sequencing methods currently under active development.

Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.

Bloom filters are space-efficient probabilistic data structures used to test whether an element is a part of a set. Bloom filters require much less space than other data structures for representing sets, however the downside of Bloom filters is that there is a false positive rate when querying the data structure. Since multiple elements may have the same hash values for a number of hash functions, then there is a probability that querying for a non-existent element may return a positive if another element with the same hash values has been added to the Bloom filter. Assuming that the hash function has equal probability of selecting any index of the Bloom filter, the false positive rate of querying a Bloom filter is a function of the number of bits, number of hash functions and number of elements of the Bloom filter. This allows the user to manage the risk of a getting a false positive by compromising on the space benefits of the Bloom filter.

<span class="mw-page-title-main">Genome skimming</span> Method of genome sequencing

Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome, to generate fragments of DNA, known as genome skims. These genome skims contain information about the high-copy fraction of the genome. The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing technology to generate these skims. Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods. Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.

References

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  2. ↑ Peltola, Hannu; Söderlund, Hans; Ukkonen, Esko (1984-01-11). "SEQAID: a DNA sequence assembling program based on a mathematical model". Nucleic Acids Research. 12 (1Part1): 307–321. doi:10.1093/nar/12.1Part1.307. ISSN   0305-1048. PMC   321006 . PMID   6320092.
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  4. ↑ Compeau, Phillip EC; Pavel A. Pevzner; Glenn Tesler (2011). "How to apply de Bruijn graphs to genome assembly". Nature Biotechnology. 29 (11): 987–991. doi:10.1038/nbt.2023. PMC   5531759 . PMID   22068540.
  5. ↑ "DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing". October 1994.
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  8. ↑ Simpson, Jared T.; et al. (2009). "ABySS: a parallel assembler for short read sequence data". Genome Research. 19 (6): 1117–1123. doi:10.1101/gr.089532.108. PMC   2694472 . PMID   19251739.
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  11. ↑ Kolmogorov, Mikhail; Yuan, Jeffrey; Lin, Yu; Pevzner, Pavel A. (2019-04-01). "Assembly of long, error-prone reads using repeat graphs" (PDF). Nature Biotechnology. 37 (5): 540–546. doi:10.1038/s41587-019-0072-8. ISSN   1087-0156. PMID   30936562. S2CID   89616540.
  12. ↑ Steinegger, Martin; Mirdita, Milot; Söding, Johannes (2019-06-24). "Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold" (PDF). Nature Methods. 16 (7): 603–606. doi: 10.1038/s41592-019-0437-4 . hdl:21.11116/0000-0003-E0DD-7. PMID   31235882.
  13. ↑ Boisvert, Sébastien; François Laviolette; Jacques Corbeil (2010). "Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies". Journal of Computational Biology. 17 (11): 1519–1533. doi:10.1089/cmb.2009.0238. PMC   3119603 . PMID   20958248.
  14. ↑ Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry; Gurevich, Alexey A.; Dvorkin, Mikhail; Kulikov, Alexander S.; Lesin, Valery M.; Nikolenko, Sergey I.; Pham, Son; Prjibelski, Andrey D.; Pyshkin, Alexey V. (May 2012). "SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing". Journal of Computational Biology. 19 (5): 455–477. doi:10.1089/cmb.2012.0021. ISSN   1066-5277. PMC   3342519 . PMID   22506599.
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  16. ↑ Chin, Chen-Shan, David H. Alexander, Patrick Marks, Aaron A. Klammer, James Drake, Cheryl Heiner, Alicia Clum et al. "Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data." Nature methods 10, no. 6 (2013): 563-569. Available online
  17. ↑ Chin, Chen-Shan, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn et al. "Phased diploid genome assembly with single-molecule real-time sequencing." Nature methods 13, no. 12 (2016): 1050-1054. Available here
  18. ↑ Koren, Sergey, Brian P. Walenz, Konstantin Berlin, Jason R. Miller, Nicholas H. Bergman, and Adam M. Phillippy. "Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation." Genome research 27, no. 5 (2017): 722-736. Available here
  19. ↑ Zimin, Aleksey V.; Marçais, Guillaume; Puiu, Daniela; Roberts, Michael; Salzberg, Steven L.; Yorke, James A. (November 2013). "The MaSuRCA genome assembler". Bioinformatics. 29 (21): 2669–2677. doi:10.1093/bioinformatics/btt476. ISSN   1367-4803. PMC   3799473 . PMID   23990416.
  20. ↑ Kamath, Govinda M., Ilan Shomorony, Fei Xia, Thomas A. Courtade, and N. Tse David. "HINGE: long-read assembly achieves optimal repeat resolution." Genome research 27, no. 5 (2017): 747-756. Available here
  21. ↑ Grabherr, Manfred G.; et al. (2011). "Full-length transcriptome assembly from RNA-Seq data without a reference genome". Nature Biotechnology. 29 (7): 644–652. doi:10.1038/nbt.1883. PMC   3571712 . PMID   21572440.
  22. ↑ Earl, Dent; et al. (December 2011). "Assemblathon 1: A competitive assessment of de novo short read assembly methods". Genome Research. 21 (12): 2224–2241. doi:10.1101/gr.126599.111. PMC   3227110 . PMID   21926179.
  23. ↑ Bradnam, Keith R.; et al. (2013). "Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species". GigaScience. 2 (1): 10. arXiv: 1301.5406 . doi: 10.1186/2047-217X-2-10 . PMC   3844414 . PMID   23870653.
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