The input sequences for est assembly are fragments of the transcribed mrna of a cell and represent only a subset of the whole genome. First, the genome is broken up into a collection of large fragments between 40 and 200 kbp called bacterial artificial chromosomes or bac s. Over the past decades dna sequencing technologies have been improving in aspects like quality, read length, runtimes and yields, all at a lower cost. Hybrid assembly approach with masurca to assemble genomes. 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 project acronym amos represents our primary goal to produce a modular, opensource whole genome assembler. Soapdenovo2 produced small contigs with a large number of errors. Masurca maryland superread celera assembler is a wholegenome assembly package that can combine short and long reads from different sequencing hardware. 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. This presentation describes masurca megareads hybrid assembly strategy and recent results on. Despite these improvements, genome assembly remains a challenge. The entire genome is fragmented and used to construct libraries of varying insert sizes.
Cabog cabog celera assembler with the best overlap graph is an assembler built upon the celera assembler, which, at first, was designed for sanger sequencing, but it was revised to handle mediumlength sequencing produced. The eight filarial nematodes that infect humans are wuchereria bancrofti, brugia malayi, brugia timori, onchocerca volvulus, loa loa, mansonella perstans, mansonella. More than 20% of the worlds population is at risk for infection by filarial nematodes and 180 million people worldwide are already infected. We apply it to the four genomes from the assemblathon competitions and. Wholegenome shotgun assembler list wgsassemblerusers. Sequencing and assembly of the 22gb loblolly pine genome. Cgview server is a comparative genomics tool for circular genomes that allows sequence feature information to be visualized in the context of sequence analysis results. Up to three comparison sequences or sequence sets in fasta format can also be submitted. 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. I think it will corrected the innieouttie designation for any libraries listed in the dncmplibraries list. Genome assembly, reconciliation and merging pipeline. 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. Currently, most genome projects use a shotgun sequencing strategy for genome sequencing fig. Masurca assembler developed at umd extending upon celera assembler.
Bioinformatics, genome assembly, genome reconciliation, genome merging, metaassembly, nextgeneration sequencing. Our assembly strategy was built around the masurca genome assembler zimin et al. Listed by phase, we report the number of bacs, and the average number and length of bactigs in genbank on september 1, 2000. 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. Ray parallel genome assemblies for parallel dna sequencing. The bacs location along the genome is then mapped using specialized laboratory experiments.
Underlying software includes jellyfish kmer counter, a modified version of the celera assembler, superreads method for extending short reads and. The bacterial sample used in this tutorial will be referred to simply as species since it is live. A genome sequence is supplied to the program in fasta, genbank, embl or raw format. Hello all, i have started the assembly with short insert and long insert and mate pair reads with 100x genome coverage. Compartmentalized assembler for the human genome table 1. Use the masurca assembler to assemble the simulated reads into a genome assembly, following the instructions given in the masurca quick start guide. Single molecule sequencing and genome assembly of a. Depending on the technology, these are sequenced independently to a given length. Salzberg1,2,3,4 1department of biomedical engineering, johns hopkins university, baltimore, md 2center for computational biology, johns hopkins university, baltimore, md 3department of computer science, whiting school of engineering, johns hopkins university. I am working on a aromatic rice genome 500mb genome. Not unexpectedly, the mmu16 dataset was more challenging than the bacterial genome.
Our developed assembler, jrassembler, uses a a strategy that selects good seeds for contig construction, b an extension strategy that uses whole sequencing reads to increase the chance to jump over repeats and to expedite extension, and c detecting. Or you want to sequence a chimp genome and you have a human already sequenced. The masurca genome assembler johns hopkins university. The problem differs from genome assembly in several ways. 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. This is the presentation that was featured on the oxford nanopore community on september 26 2017. I am asking because i had some luck using the spades assembler to assemble the mitochondrial genome from subsamples of full genomic reads of parasitic nematodes, but it. The key idea in masurca is to reduce highcoverage pairedend reads to a much smaller and more concise set of superreads. The basic concepts of genome assembly published on october 14, 2015 in genomics sequence analysis by muniba faiza genome, as we all know, is a complete set of dna in an organism including all of its genes. Genome assembly genome assembly is the process of determining an organisms dna. Usually, a single draft assembly is selected as the candidate for publication. Hybrid assembly of the large and highly repetitive genome. The genome polishing tool polca makes fast and accurate. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task.
We use this method to produce an assembly of the large and complex genome of. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. Celera assembler is an algorithm to produce a set of haploid consensus sequences rather than a single consensus sequence. We call our system the maryland superread celera assembler abbreviated masurca and pronounced mazurka. Whole genome assembly and alignment michael schatz oct 25, 2012 cshl sequencing course. A database providing information on the structure of assembled genomes, assembly names and other metadata, statistical reports, and links to genomic sequence data. 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. Software engineers who write assembly programs know they need to adapt. Used to identify overlaps essentially unique dna sequences physical markers are used to build a physical map. 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. In a first step, genomic dna is sheared into small random fragments.
From the university of maryland assembly group website. Two or more clones that can be shown to overlap make a contig physical markers. Ray assembles reads obtained with new sequencing technologies illumina, 454, solid using mpi 2. It facilitates downstream data analysis by relieving investigators from the burdens of data preparation. Institute for physical sciences and technology, university of maryland, college park, md 20742.
Identifies allelic variation given a whole genome shotgun wgs assembly of haploid sequences. Typically there are libraries of some smaller size 2, 4 or 6 kb, libraries of intermediate size 10 40 kb and libraries with large insert sequences 100 kb. 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 tutorial will serve as an example of how to use free and opensource genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. A field guide to wholegenome sequencing, assembly and. So far i have tried abyss, idbaud, platanus, soap and masurca. The masurca assembler tgz archive has already been unpacked, compiled, and installed in the usrlocal masurca directory of the vcl machine image. Emerson these authors contributed equally to whom correspondence should be addressed. Masurca can assemble data sets containing only short reads from illumina sequencing or a mixture of short reads and long reads sanger, 454. The following is required all current major linux distributions include. The whole genome assembly wga approach, which is the dominant strategy in use today, dispenses with up front mapping. It uses a dynamic windowing approach and detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation.
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