The masurca assembler has been developed by the pinerefseq team at umd specifically for assembling such large genomes. The sequencing and assembly strategy described here, of the largest genome to date, resulted in a haploid assembly composed of 20. Genome sequencing of a single tardigrade hypsibius. By many measures, it is the most contiguous and complete draft assembly of a conifer genome appendix c. Reducing assembly complexity of microbial genomes with. Masurca requires illimina data, and it now supports thirdgeneration pacbionanopore minion reads for hybrid assembly. We evaluate the performance of masurca against two of the most widely used assemblers for illumina data, allpathslg and soapdenovo2, on two datasets from organisms for which highquality assemblies are available. Nov 01, 20 read the masurca genome assembler, bioinformatics on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. Hybrid genome assembly and annotation of danionella. 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. Zimin av, puiu d, luo mc, zhu t, koren s, yorke ja, dvorak j, salzberg s. The spades assembler came in first for the other two genomes, and was a close second for an additional two organisms.
Hello all, i have started the assembly with short insert and long insert and mate pair reads with 100x genome coverage. The problem differs from genome assembly in several ways. Hybrid assembly of the large and highly repetitive genome of aegilops tauschii, a progenitor of bread wheat, with the megareads algorithm. The masurca assembler tgz archive has already been unpacked, compiled, and installed in the usrlocalmasurca directory of the vcl machine image. In our manual analysis of the connexin genes we first identified 51 herring connexin genes from the draft assembly by martinez barrio et al of. In other words, each kmer in the genome is represented by two nodes in the graph connected by an edge. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Masurca had the largest contig sizes, measured by either n50 or corrected n50 values, for ten of the twelve genomes.
We use this method to produce an assembly of the large and complex genome of. Using a genomesize estimate of 22 gbp for loblolly pine, this represents 7. Underlying software includes jellyfish kmer counter, a modified version of the celera assembler, superreads method for extending short reads and. The megareads software, which is now incorporated into the masurca assembler, can handle hybrid assemblies of almost any plant or animal genome. The megareads software, which is now incorporated into the masurca assembler, can handle hybrid assemblies of almost any plant or animal. Use the masurca assembler to assemble the simulated reads into a genome assembly, following the instructions given in the masurca quick start guide. Secondgeneration sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. We call our system the maryland superread celera assembler abbreviated masurca and pronounced mazurka. Genome assembly of six polyploid potato genomes scientific data. Such a large number of mismatches in the contigs will induce less overlaps between the reads and these. In terms of assembly errors, the celera assembler produced none and no assembler had more than three. Such low deviations from the target library size may not be typical for all sequencing centers and genome projects. Sequencing and assembly of the 22gigabase genome of.
High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. First, the genome is broken up into a collection of large fragments between 40 and 200 kbp called bacterial artificial chromosomes or bac s. Read the masurca genome assembler, bioinformatics on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. How we measure reads a read is counted each time someone views a publication.
This project required a close coupling between sequencing and assembly strategy and the. Both spades and masurca assemblies were polished using icorn 53. Institute for physical sciences and technology, university of maryland, college park, md 20742, usa, center for computational biology, mckusicknathans institute of genetic medicine, johns hopkins university school of medicine, baltimore, md 21205, usa, department of mathematics and department of physics, university of maryland, college park, md 20742, usa. The key idea in masurca is to reduce highcoverage pairedend reads to a much smaller and more concise set of superreads. We show that masurca performs on par or better than allpathslg and significantly better than soapdenovo on these data, when evaluated against the finished sequence. The masurca genome assembler johns hopkins university. Institute for physical sciences and technology, university of maryland, college park. However, from the busco manual, the only valid value for the lineage parameter seems to.
The loblolly pine genome project lpgp is part of the usdafunded pinerefseq project whose aim is. The masurca assembler benefits from the advanced assembly techniques in the cabog assembler for creating contigs and scaffolds from superreads. Following the creation of draft versions of the human genome in 2001, many small and large. I am working on a aromatic rice genome 500mb genome. Pdf the masurca genome assembler james yorke academia. From the university of maryland assembly group website. Sequencing and assembly of the 22gb loblolly pine genome. Masurca maryland superread celera assembler is a wholegenome assembly package that can combine short and long reads from different sequencing hardware. 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. 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. Mar 11, 2020 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. 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.
The performance of the masurca assembler was genome and data dependent, as it generated poor assembly statistics for strain bt03 and gm30 while reasonable assembly statistics for strain cf080 and gm41 supplementary table s3. The university of maryland genome assembly group developing methods for improving genome assembly. The input sequences for est assembly are fragments of the transcribed mrna of a cell and represent only a subset of the whole genome. Down sampling with the fastq toolkit, is an optional step that can be used if more than 1 gigabase is generated for any organism. The masurca assembly generated only one gap when aligned to the reference and a 99. Overall, masurca and spades produced the best assemblies across these twelve bacterial organisms.
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. Saw this tweet this morning and thought this would be good to try out for our olympia oyster genome assemblies, as it will handle hybrid assemblies i. Genome assembly primer our genetic heritage, as well as that of all living organisms, is encoded in a set of dna molecules called chromosomes. The masurca assembler uses a modified version of the cabog assembler for contiging and scaffolding, and in practice it will produce good assemblies with libraries whose standard deviations are up to 20% of the library mean. Masurca maryland superread celera assembler genome assembly software.
You can access the human genome from any computer by going to. The masurca assembler tgz archive has already been unpacked, compiled, and installed in the usrlocal masurca directory of the vcl machine image. Introduction to masurca genome assembler bioinformatics. The bacs location along the genome is then mapped using specialized laboratory experiments. The mp100k for masurcas hiseq assembly, basic flow for of r. Table 1 shows the comparison of the performance of the masurca assembler with the others on the r. Mar 01, 2014 using a genomesize estimate of 22 gbp for loblolly pine, this represents 7. Assembly and mapping of sequenced reads for technical validation. Masurca is distributed under an open source gplv3 license. Institute for physical sciences and technology, university of maryland, college park, md 20742. Sequencing and assembly of the 22gigabase genome of loblolly. Masurca uses a modified version of the cabog assembler miller et al.
Pdf secondgeneration sequencing technologies produce high coverage of the genome by short reads at a very low cost, which has prompted development of. Results we evaluate the performance of masurca against two of the most widely used assemblers for illumina data, allpathslg and soapdenovo2, on two datasets from organisms for which highquality assemblies are available. Use the masurca assembler to assemble the simulated reads into a genome assembly, following the instructions given. Our assembly strategy was built around the masurca genome assembler zimin et al. Argane, argania spinosa, endemic, genome, assembly, morocco. Nowadays genome analysis is an important part of the microbiological research and microbiologists can launch genome projects cheaper than ever before van dijk et al. Zimin av1, marcais g, puiu d, roberts m, salzberg sl, yorke ja. 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. Because the minimum range of size selection was 400 bp, insert size without illumina adapters roughly corresponds to this length. In recent years, the advent of ngs has revolutionized the biological sciences and other technologies, especially with regard to genome studies ansorge, 2009, maclean et al. Masurca genome assembler bioinformatics oxford academic.
Hybrid assembly of the large and highly repetitive genome of. Spades generated two gaps while dnastar produced five gaps. The masurca maryland super read cabog assembler genome assembly and. Masurca requires a configuration file that states the type of data you have and the parameters you want to use in your run. The masurca genome assembler article pdf available. The key idea in masurca is to reduce highcoverage pairedend reads to a. While the inclusion of fosmid ditag libraries was helpful, only approximately onethird of the v1.
Written and maintained by simon gladman melbourne bioinformatics formerly vlsci. Masurca is the maryland superread celera assembler and can be used on assembly projects of all sizes, from bacteria genomes to mammalian genomes to large plant genomes. 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. Hybrid assembly of illumina and nanopore reads is one of the new features of the masurca assembler, version 3. Aug 26, 2019 our assembler of choice was masurca v3. Comparison of genome sequencing technology and assembly. See the github page for more information on the configuration file specific to your particular input files. Dec 06, 20 high genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. 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. 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. Nov, 20 the sequencing and assembly strategy described here, of the largest genome to date, resulted in a haploid assembly composed of 20. So far i have tried abyss, idbaud, platanus, soap and masurca. Masurca can assemble data sets containing only short reads from illumina sequencing or a mixture of short reads and long reads sanger.
First draft genome assembly of the argane tree argania. Decoding the massive genome of loblolly pine using haploid. Masurca is a whole genome assembly software that can assemble data sets. Masurca assembler developed at umd extending upon celera assembler. Ethical, legal and social implication with the powerful new tools of genomics, society needs to look carefully at.
Each such molecule can be represented as a string of just four letters. I have started the assembly with short insert and long insert and mate pair reads with 100x genome coverage. Masurca is based on the celera assembler and uses an overlaplayoutconsensus approach with kunitigs and superreads which allows for a 100fold data reduction. The final draft genome comprises 75 327 scaffolds totaling 671 mb with an n50 of 49 916 kb.
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