Aggressive assembly of pyrosequencing reads with mates

Miller, Jason R.; Delcher, Arthur L.; Koren, Sergey; Venter, Eli; Walenz, Brian P.; Brownley, Anushka; Johnson, Justin; Li, Kelvin; Mobarry, Clark; Sutton, Granger

doi:10.1093/bioinformatics/btn548

Cited by 500 publications

(475 citation statements)

References 29 publications

(35 reference statements)

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“…For each species, a single paired-end library was sequenced to 9-39× coverage on the Illumina HiSeq 2000 platform (Supplementary Table 2 and Supplementary Note). The genome sequences were assembled with the Celera Assembler 26 , resulting in N50 scaffold sizes between 3.2 and 71 kb (Supplementary Table 3 and Supplementary Note). For most species, we recovered more than 75% of the conserved eukaryotic genes included in the CEGMA 27 analysis, and on average we recovered 74% of the conserved genes of the Actinopterygii data set included in the BUSCO 28 analysis.…”

Section: Sequencing and Draft Assembly Of 66 Teleost Genomesmentioning

confidence: 99%

Evolution of the immune system influences speciation rates in teleost fishes

et al. 2016

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With over 32,000 extant species 1 , teleost fishes comprise the majority of vertebrate species. Their taxonomic diversity is matched by extensive genetic and phenotypic variation, including novel immunological strategies. Although the functionality of the adaptive immune system has been considered to be conserved since its emergence in the ancestor of all jawed vertebrates 2,3 , fundamental modifications of the immune gene repertoire have recently been reported in teleosts [4][5][6][7] . One of the most dramatic changes has occurred in Atlantic cod (Gadus morhua), involving complete loss of the MHC II pathway that is otherwise responsible for the detection of bacterial pathogens in vertebrates 4 . Moreover, this loss is accompanied by a substantially enlarged repertoire of MHC I genes, which normally encode molecules for protection against viral pathogens. It has thus been hypothesized that the expanded MHC I repertoire of cod evolved as a compensatory mechanism, whereby broader MHC I functionality makes up for the initial loss of MHC II (refs. 4,6). However, the questions of how and when MHC II was lost relative to the MHC I expansion, and whether these genomic modifications are causally related, have so far remained unresolved.As key components of the vertebrate adaptive immune system, the complex MHC pathways and their functionality are now well characterized 8-10 , but less is known about the causes of MHC copy number variation, which poses an immunological tradeoff 11,12 . Although an increase in the number of MHC genes facilitates pathogen detection, it will also decrease the number of circulating T cells [13][14][15][16] , resulting in an immune system that can detect a large number of pathogens at the expense of being less efficient in removing them. The evolution of MHC copy numbers is therefore likely driven toward intermediate optima determined by a tradeoff between detection and elimination of pathogens-as suggested by selection for 5-10 copies inferred in case studies of fish 17,18 and birds 19 . Because pathogen load and the associated selective pressures vary between habitats, the optimal number of MHC copies depends on the environment [20][21][22] . As a result, interbreeding between different locally adapted populations is expected to produce hybrids with excess (above optimal) MHC diversity that are characterized by T cell deprivation and low fitness. This process would introduce postzygotic reproductive isolation and promote reinforcement of premating isolation between the populations. Consequently, MHC genes have been suggested to have an important role in speciation 22,23 , but, to our knowledge, this role has never been tested comparatively in a macroevolutionary context.Here we report comparative analyses of 76 teleost species, of which 66 were sequenced to produce partial draft genome assemblies, including 27 representatives of cod-like fishes within the order Gadiformes. First, we use phylogenomic analysis to resolve standing controversy regarding early-teleost divergences and to firmly ...

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Section: Sequencing and Draft Assembly Of 66 Teleost Genomesmentioning

confidence: 99%

Evolution of the immune system influences speciation rates in teleost fishes

et al. 2016

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“…It provides better and more preferable performance in terms of speed and output quality 44 compared with the other tools mentioned above. The second category of software that includes CABOG, 45 Edena, 46 Newbler 47 and Shorty 48 are based on overlap-layout-consensus. This strategy involves three main steps.…”

Section: Assembly Strategiesmentioning

confidence: 99%

“…Newbler, among the overlap-layout-consensus-based software, was specifically designed to handle the ambiguity in the length of 454's homopolymer runs, whereas the other widely used programs (distributed by Illumina/Solexa), including Shorty, can also be applied to 49,50 whose main procedure could be summarized as 'unitig-contig-scaffolds' , for base call correction. 45 Shorty innovatively estimates the intercontig distances from the mate pairs using a few seeds of 300-500 bp length. The third category of software based on de Bruijn graph approaches 40 are widely used in assembling data from the Solexa and SOLiD platforms.…”

Section: Assembly Strategiesmentioning

confidence: 99%

Evaluation of next-generation sequencing software in mapping and assembly

et al. 2011

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Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.

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“…As an example, Figure 3 shows the Hawkeye LaunchPad for an assembly of the 2.9-Mb Staphylococcus aureus genome available on the AMOS website (http://sourceforge.net/projects/amos/files/sample_data/). The genome was assembled using the pre-assembly error correction program Quake [25] and the Celera Assembler [3] from $25Â coverage of 100-bp reads sequenced at the Broad Institute using an Illumina Genome Analyzer II (SRA study SRP001086). These mated reads were sequenced using a combination of $20Â coverage of a 165-bp fragment library, and $5Â coverage of a 3.5-kb jumping library.…”

Section: Technologies and Features Visual Assembly Analytics With Hawmentioning

confidence: 99%

“…Over the years, numerous genome assemblers have been developed, among which we highlight just a few of the most memorable: phrap-one of the most widely used assemblers of the first generation sequencing era; Celera Assembler [2,3]-the software originally developed at Celera Genomics and used to assemble the human genome through a whole-genome shotgun sequencing approach (as opposed to the BAC-by-BAC approach employed by the Human Genome Consortium); Velvet [4]one of the first among a number of assemblers developed specifically for second generation sequencing data; and ALLPATHS-LG [5]-perhaps the most effective genome assembler for second generation sequencing data today. These, and the many other assemblers used in the community, have contributed to the reconstruction of tens of thousands of viruses and bacteria, as well as hundreds of eukaryotes, including the genomes of many mammals (human [6], mouse [7], cow [8], panda [9], etc.…”

Section: Introduction and Contextmentioning

confidence: 99%

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

Schatz

Phillippy²,

Sommer

et al. 2011

Briefings in Bioinformatics

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Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second-and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net.

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Aggressive assembly of pyrosequencing reads with mates

Cited by 500 publications

References 29 publications

Evolution of the immune system influences speciation rates in teleost fishes

Evolution of the immune system influences speciation rates in teleost fishes

Evaluation of next-generation sequencing software in mapping and assembly

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

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