The masurca genome assembler pdf engineer

This presentation describes masurca megareads hybrid assembly strategy and recent results on. Genome assembly is a fundamental problem with multiple applications. I am working on a aromatic rice genome 500mb genome. Underlying software includes jellyfish kmer counter, a modified version of the celera assembler, superreads method for extending short reads and. The input sequences for est assembly are fragments of the transcribed mrna of a cell and represent only a subset of the whole genome. Hybrid assembly of the large and highly repetitive genome of. The following is required all current major linux distributions include. That is not going to work, its a ca option not a masurca option.

First draft assembly and annotation of the genome of a. Esmail foroozan at national institute of genetic engineering and. It might work on other unix like systems but it is not well tested. Here we report the new chromosomescale assembly 32 of the walnut reference genome chandler v2. We call our system the maryland superread celera assembler abbreviated masurca and pronounced mazurka. The size and complexity of their genomes has presented formidable technical challenges for whole genome shotgun sequencing and assembly. Here, we report on efforts to generate a more complete genome assembly for l. Although there are several assembly algorithms developed for data generated with different sequencing technologies, and some that can make use of hybrid data, the assemblies are still far from being perfect. In this paper, we propose a new computer algorithm for dna sequence assembly that combines in a novel way the techniques of both shotgun and sbh methods. Wholegenome shotgun assembler list wgsassemblerusers. The douglasfir genome sequence reveals specialization of. Academic and professional experience 2011present professor, department of medicine and the mckusicknathans institute of genetic medicine, johns hopkins university. Zimin av1, marcais g, puiu d, roberts m, salzberg sl, yorke ja.

Masurca maryland superread celera assembler is a whole genome assembly package that can combine short and long reads from different sequencing hardware. Affiliation school of computer science and engineering, pusan national. Based on our preliminary investigations, the algorithm promises to be very fast and practical for dna sequence assembly. Improving genome assemblies using multiplatform sequence. 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. 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 hybridhierarchical genome assembly strategy to sequence. Draft genome sequence of sugiyamaella xylanicola ufmgcm.

P3 was isolated from agricultural soil from the badaun midwestern plain zone region of uttar pradesh, india. We employed novel strategies that allowed us to determine the loblolly pine pinus taeda reference genome sequence, the largest genome assembled to date. The mp100k for masurca s hiseq assembly, basic flow for of r. All reads were generated from the chinese spring variety cs42, accession dv418 of t. Masurca is a whole genome assembly software that can assemble data sets.

Assessing the quality of these assemblies and comparing those produced by different tools is essential in choosing the best ones. We use this method to produce an assembly of the large and complex genome of. 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. A new algorithm for dna sequence assembly journal of. Assembly of a pan genome from 910 humans of african descent identifies 296.

Thus, the masurca gap closer is able to close gaps that are longer than a read, but shorter than the length of a fragment for illumina pairedend reads. Highquality chromosomescale assembly of the walnut. 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. Current technological limitations do not allow assembling of entire genomes and many programs have been designed to produce longer and more reliable contigs. The assembled draft genome consisted of,714,239 bp distributed across 1251 contigs longer than 272 bp and a gc content of 33. Assembly of a pangenome from deep sequencing of 910. Brie y, the velvet assembly using only the illumina reads showed better coverage 99% and high average identity 97. Not unexpectedly, the mmu16 dataset was more challenging than the bacterial genome. Whole genome sequencing was carried out by macrogen, inc. Here we describe the sequencing and assembly of the pathogenic fungus lomentospora prolificans using a combination of short, highly accurate illumina reads and additional coverage in very long oxford nanopore reads. You should contact the masurca support team instead. To obtain the best assembly, numerous assemblers and sequencing datasets were analyzed, combined, and compared.

We also used two hybrid assemblers, celeracabog 5 and masurca 6 on the same data to compare our correction methodology with those of hybrid assembly algorithms. The problem differs from genome assembly in several ways. Draft genome sequences of rhodosporidium toruloides. Masurca can assemble data sets containing only short reads from illumina sequencing or a mixture of short reads and long reads sanger, 454. Single molecule sequencing and genome assembly of a.

Hybrid assembly of the large and highly repetitive genome. I am now updating the masurca manual to reflect the new options for grid execution, and i will upload it later today. These facts make prokaryote genome assembly a more tractable problem than eukaryote genome assembly, and in most cases a longread set of sufficient depth should contain enough information to generate a complete assembly each replicon in the genome being fully assembled into a single contig7. Hybrid assembly approach with masurca to assemble genomes. We first used simulated human data to compare the sensitivity and precision of stringtie2, with and without superreads, to that of scallop fig. Most of the sequence data were derived from whole genome. Institute for physical sciences and technology, university of maryland, college park, md 20742. Masurca requires illimina data, and it now supports thirdgeneration pacbionanopore minion reads for hybrid assembly. For assembly with illuminaonly data, the nga50 contig size for masurca assembly was twice as big compared with the allpathslg assembly, whereas the number of errors was 62% larger. Secondgeneration sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. The university of maryland genome assembly group developing methods for improving genome assembly.

The masurca genome assembler johns hopkins university. Masurca maryland superread celera assembler genome assembly software. Such a large number of mismatches in the contigs will induce less overlaps between the reads and these. Using just pacbio reads from a long insert library, the reads are often preprocessed before being assembled using an overlaplayoutconsensus algorithm.

The megareads software, which is now incorporated into the masurca assembler, can handle hybrid assemblies of almost any plant or animal. Genome assembly of polyploid plant genomes is a laborious task as they contain more than two copies of the genome, are often highly heterozygous with a high level of repetitive dna. This is the presentation that was featured on the oxford nanopore community on september 26 2017. The first nearcomplete assembly of the hexaploid bread wheat.

The resulting assembly is highly contiguous, containing a total of 37,627,092 bp with over 98% of the sequence in just 26 scaffolds. Soapdenovo2 produced small contigs with a large number of errors. Draft genome sequence of bacillus marisflavi cknbri03. So far i have tried abyss, idbaud, platanus, soap and masurca. Are you specifying dofragmentcorrection0 in the masurca config. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. First draft genome sequence of the pathogenic fungus. We apply it to the four genomes from the assemblathon competitions and. Benchmarking of longread assemblers for prokaryote whole.

Sequencing and assembly of the 22gb loblolly pine genome. Departments of biomedical engineering, computer science, and biostatistics. This african pan genome contains 10% more dna than the. 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. Hello all, i have started the assembly with short insert and long insert and mate pair reads with 100x genome coverage. Joint appointments as professor in the department of biostatistics, bloomberg school of public health, and in the department of computer science, whiting school of engineering. Thanks to daniela puiu, the software engineer at the center for.

Secondgeneration sequencing technologies produce high coverage of the genome by short reads at a low cost, which has. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded genes. Masurca 6 on the same data to compare our correction methodology with those of hybrid assembly algorithms. Whole genome shotgun assembler mailing lists brought to you by. This lets us compare the polished assembly to the true genome. Relative to the 34 previous reference genome, the new assembly features an 84. Masurca is distributed under an open source gplv3 license. 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. Our pipeline can reduce the time spent on the manual tasks required for.