The masurca genome assembler pdf english

English ac, richards s, han y, wang m, vee v, qu j, qin x, muzny dm, reid jg. Masurca can assemble data sets containing only short reads from illumina sequencing or a mixture of short reads and long reads sanger, 454, pacbio and nanopore. This is needed as dna sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. The problem differs from genome assembly in several ways. A highresolution snp arraybased linkage map anchors a new. The 2011 german outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. This is the presentation that was featured on the oxford nanopore community on september 26 2017.

A cluster can be used as well, but the main execution node must meet the ram requirements. Sanger sequence data, multiple genetic linkage and rh maps, and. First draft assembly and annotation of the genome of a. Masurca genome assembler bioinformatics oxford academic. Masurca whole genome assembler software versions introduction masurca maryland superread celera assembler is a wholegenome assembly package that can combine short and long reads from different sequencing hardware. Hello all, i have started the assembly with short insert and long insert and mate pair reads with 100x genome coverage. To prepare an input assembly graph for cerulean, we employed abyss, which is an assembler for short reads, and used kmer 62. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded genes.

This african pan genome contains 10% more dna than the. Genome assembly primer our genetic heritage, as well as that of all living organisms, is encoded in a set of dna molecules called chromosomes. And, of course, genome assembly is becoming even more complex because it used to be that assembling the human genome was the big task scientifically in front of the community. It consists of all the heritable information and also some regions which are not even expressed. Introduction the persian walnut english or common walnut. So far i have tried abyss, idbaud, platanus, soap and masurca. Hybrid assembly of the large and highly repetitive genome. We use this method to produce an assembly of the large and complex genome of.

Expressed sequence tag or est assembly was an early strategy, dating from the mid1990s to the mid2000s, to assemble individual genes rather than whole genomes. A nonhybrid assembly method hgap has been developed that requires 80100. We apply it to the four genomes from the assemblathon competitions and. We assembled over 86 % 389 mb of rice genome and annotated 56,284 proteincoding genes from hr12 genome using illumina and pacbio sequencing. A draft nucleargenome assembly of the acoel flatworm. Opensource so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. It is the only unique member of the tropical sapotaceae family in morocco 3. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits. The university of maryland genome assembly group developing methods for improving genome assembly. It might work on other unix like systems but it is not well tested. Table 1 shows the comparison of the performance of the masurca assembler with the others on the r. Assembly of a pan genome from 910 humans of african descent identifies 296. In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer dna sequence in order to reconstruct the original sequence. The performance of the masurca assembler was genome and data dependent.

Masurca is the only assembler designed for very large genomes having been successfully applied to the 22 gb loblolly pine genome 37, however, we have had difficulty applying this software to polymorphic insect genomes from 2. Mar 29, 2016 the domestic cat genome assembly is unique among many other mammalian genome assemblies, being based on a large variety of sequencing read lengths, including a combination of legacy and ngs technology, and is anchored by a variety of physical mapping resources, including 2. Reducing assembly complexity of microbial genomes with. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases mb. Assembly of a pangenome from deep sequencing of 910 humans. Software tools which carry out assembly assemblers take sequencing reads as input and produce reconstructed contiguous pieces of the genome contigs as output. Institute for physical sciences and technology, university of maryland, college park, md 20742. Sep 24, 2015 genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses.

In the context of assembly we are looking at the subgraph of the complete debruijn graph that contains just the kmers present in the genome as inferred from the set of reads. The masurca assembler using only illumina data performs on par with allpathslg, with nearly identical nga50 sizes, two fewer contig errors and two more scaffold errors. Forth, every genome assembly is the result of a series of assembly heuristics and should accordingly be treated as a working hypothesis. N50 is the minimum scaffoldcontig length needed to cover 50% of the genome. You can access the human genome from any computer by going to. The opensource masurca maryland superreads with celera assembler genome assembly software has been under development at the university of maryland and johns hopkins university since 2011, with recent work focusing on assembly of hybrid data sets zimin et al. Underlying software includes jellyfish kmer counter, a modified version of the celera assembler, superreads method for extending short reads and. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. The project acronym amos represents our primary goal to produce a modular, opensource whole genome assembler. To resolve these regions, we exploited a new whole genome assembly algorithm, the jr assembler, which compares favorably to current assemblers in terms of quality, efficiency, and memory.

Mar 16, 2016 in this study, we generated deepsequencing data illumina and pacific biosciences sequencing for one of the indica rice cultivars, hr12 from india. Rna sequencing and isoseq data from embryos, larvae, and adults were also obtained. Written and maintained by simon gladman melbourne bioinformatics formerly vlsci. We resequenced the best195 genome using a pacbio rs sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied illumina miseq short reads to enhance quality. Nov 19, 2018 assembly of a pan genome from 910 humans of african descent identifies 296. The following is required all current major linux distributions include. Academic and professional experience 2011present professor, department of medicine and the mckusicknathans institute of genetic medicine, johns hopkins university.

Additional research is required to address this problem. We describe here a novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer. The argane tree forest was recognized as biosphere reserve arganeraie biosphere reserve by unesco in 1998 2. We apply it to the four genomes from the assemblathon competitions and show it. I have started the assembly with short insert and long insert and mate pair reads with 100x genome coverage. This paper reports progress in assembling genomes facili tated by a new approach to genome assembly. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Sep 27, 2017 this is the presentation that was featured on the oxford nanopore community on september 26 2017. Masurca maryland superread celera assembler is a whole genome assembly package that can combine short and long reads from different sequencing hardware. The genome of indica rice cultivar, hr12 was assembled using combination of short reads pe and mp libraries from illumina and long reads additional file 2 from pacific biosciences additional file 3. The megareads software, which is now incorporated into the masurca assembler, can handle hybrid assemblies of almost any plant or animal genome, including genomes as large as the 22 gbp loblolly pine.

Assembly of a pangenome from deep sequencing of 910. This african pan genome contains 10% more dna than the current. Indica rice genome assembly, annotation and mining of. Although over 80 % of rice cultivation in the world under indica rice cultivation however, genomic resources are lacking for this subspecies. Subanguina moxae, belonging to the subfamily anguininae, is an obligate parasite of artemisia plants, which are widely used as cooking herbs and in traditional medicine in east asia. The masurca algorithm is designed to be able to perform a 30 gbp plant genome assembly on one computer with 2 tb of ram. Hybrid assembly approach with masurca to assemble genomes. A busco assessment found 88% of metazoan orthologs present in the genome. Thus, we and other researchers believe that creating an indica reference rice genome is essential for genome wide studies, which will enable genome assisted indica rice breeding program.

Apr 18, 2016 the genome sequence is presented for the atlantic salmon salmo salar, providing information about a rediploidization following a salmonidspecific whole genome duplication event that resulted in. Whole genome complete resequencing of bacillus subtilis natto. We present an octocoral genome assembly and showcase the feasibility of the masurca hybrid assembler for marine invertebrate genomics. Genome assembly is the process by which an unknown genome sequence is. Because the nematode is distributed throughout east russia and east asia, there is concern about the potential for significant damage to commercial farming. We call our system the maryland superread celera assembler abbreviated masurca and pronounced mazurka. Recently, the first genome assembly of gayal, mithun of chinese origin, was published. Thus, a genome of the octocoral renilla is highly valuable to the scientific. The masurca genome assembler johns hopkins university. Ethical, legal and social implication with the powerful new tools of genomics, society needs to look carefully at. Genomics, bioinformatics, genome assembly, gene finding, sequence analysis algorithms. We sequenced indica cultivars, which are highly resistant tetep and tadukan and susceptible hr12 and co39 to rice blast disease caused by ascomycetes pathogen magnaporthe oryzae fig.

Masurca can assemble data sets containing only short reads from illumina sequencing or a mixture of short reads and long reads sanger. Soapdenovo2 produced small contigs with a large number of errors. Our hybrid assembly algorithm combines these two types of reads to construct. Masurca maryland superread celera assembler genome assembly software. Currently, most genome projects use a shotgun sequencing strategy for genome sequencing fig.

The input sequences for est assembly are fragments of the transcribed mrna of a cell and represent only a subset of the whole genome. Another approach to assembly, which has become possible with the advent of increasing numbers of finished genomes, is comparative assembly, in which a reference genome is used to guide assembly. A roadmap to the denovo assembly of the banana slug. Masurca is distributed under an open source gplv3 license. L50 is the number of contigs required to reach n50. Not unexpectedly, the mmu16 dataset was more challenging than the bacterial genome. In particular, assemblies generated by wengan, masurca or wtdbg2 were. Whole genome complete resequencing of bacillus subtilis. Skeels is a tree endemic to the south west of morocco and occupying arid and semiarid regions totaling up to around 900,000 ha 1.

But now there are billions of genomes waiting to be sequencedall the individuals in the world and to try and interpret them. Each such molecule can be represented as a string of just four letters. Masurca can assemble data sets containing only short reads from illumina sequencing or a mixture of short reads and long reads sanger, 454. This african pan genome contains 10% more dna than the current human reference genome. Almost 98 % of human genome has been sequenced by the human genome project, only 1 to 2 % has been understood. The megareads software, which is now incorporated into the masurca assembler, can handle hybrid. Hybrid assembly of the large and highly repetitive genome of. Pacbio subreads were assembled with sprai version 0. Dec 23, 2019 genome assembly is the computational process of using shotgun wholegenome sequencing data reads to reconstruct an organisms true genomic sequence to the greatest extent possible 1.

Zimin av1, marcais g, puiu d, roberts m, salzberg sl, yorke ja. I am working on a aromatic rice genome 500mb genome. Manual annotation and use of additional data, such. To construct a new genome assembly we utilized all existing genomic data generated from cinnamon, a female abyssinian cat used for all prior genome assemblies pontius et al. Both spades and masurca assemblies were polished using icorn 53. Here we introduce a draft genome assembly of valley oak quercus lobata using illumina sequencing of adult leaf tissue of a tree found in an accessible, wellstudied, natural southern california population. Currently gold standard assembly and annotation are available for japonica rice. Student in computer science university of wurzburg, germany university of applied sciences western switzerland. In other words, each kmer in the genome is represented by two nodes in the graph connected by an edge. The final draft genome comprises 75 327 scaffolds totaling 671 mb with an n50 of 49 916 kb. Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses.

Masurca is the only assembler designed for very large genomes having been successfully applied to the 22gb loblolly pine genome, however, we have had difficulty applying this software to polymorphic insect genomes from 2. Benchmarking of longread assemblers for prokaryote. A highresolution snp arraybased linkage map anchors a. Kmer i have given as auto so its running with 31 kmer and work2. In a first step, genomic dna is sheared into small random. Like dickens, we must computationally reconstruct a genome from short. This presentation describes masurca megareads hybrid assembly strategy and recent results on. Masurca requires illimina data, and it now supports thirdgeneration pacbionanopore minion reads for hybrid assembly. Emerson these authors contributed equally to whom correspondence should be addressed. Oct 14, 2015 genome, as we all know, is a complete set of dna in an organism including all of its genes. Motivation secondgeneration sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. Indica rice genome assembly, annotation and mining of blast.