Sequencing

Recommendations

Info

11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting RECENT ADDITIONS TO SPADES FAMILY OF TOOLS FOR GENOME ASSEMBLY AND ANALYSIS Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.21) Alla Lapidus,. Dmitry Antipov, Anton Bankevich, Elena Bushmanova, Alexey Gurevich, Anton Korobeynikov, Alla Mikheenko, Dmitry Meleshko, Sergey Nurk, Andrey Prjibelski, Yana Safonova, Pavel Pevzner Saint Petersburg State University Despite its central role in genomics, accurate de novo genome assembly remains challenging. Moreover, the proliferation of new sequencing and sample‐preparation technologies introduces additional levels of complications. In 2015, the SPAdes genome assembler (Bankevich et al., 2012), that was originally conceived as a scalable and easy‐to‐modify platform, was gradually extended into a family of SPAdes tools aimed at various sequencing technologies and applications. In addition to the constantly updated SPAdes assembler itself, it now includes: metaSPAdes assembler for metagenomics data (Nurk et al., 2015) rnaSPAdes: de novo RNA‐seq data assembler (Prjibelsky et al., submitted) plasmidSPAdes: assembly of plasmids from the whole genome sequencing data (Antipov et al., submitted) dipSPAdes tool for assembly of highly polymorphic genomes (Safonova et al., 2015) exSPAnder module for repeat resolution that enables efficient utilization of mate‐pair libraries and even mate‐pairs only assemblies with NexteraMP libraries (Prjibelsky et al., 2014, Vasilinetc et al., 2015) hybridSPAdes tool for hybrid assembly of accurate short reads with long error‐prone reads, such as Pacific Biosciences and Oxford Nanopore reads (Antipov et al., 2015) truSPAdes tool for assembling Illumina’s barcoded True Synthetic Long Reads (Bankevich and Pevzner, 2015) We will provide an overview of the SPAdes family of tools and benchmark them against state‐of‐theart assembly tools using the QUAST family of assembly evaluation tools: • QUAST tool for the quality assessment of genomics assemblers (Gurevich et al., 2013) • metaQUAST tool for the quality assessment of metagenomics assemblers (Mikheenko et al., 2015) • rnaQUAST tool for the quality assessment of RNA‐Seq metagenomics assemblers (Bushmanova et al., 2015) 55
11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting A DRAFT GENOME OF THE RESURRECTION LYCOPHYTE SELAGINELLA ARIZONICA SELAGINELLACEAE Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.22) Anthony Baniaga,. ThiruvaranganRamaraj 2 , Tara Hall 1 . Nils Arrigo 3 , Michael Barker 1 1 University of Arizona, Department of Ecology & Evolutionary Biology, 2 National Center for Genome Resources (NCGR), 3 University of Lausanne, Department of Ecology & Evolution Selaginella spp. Selaginellaceae have the potential to become an interesting model system to understand local adaptation and the evolutionary genetics associated with whole genome duplication and hybridization. They possess some of the smallest known genomes (1Cx = 81‐182 Mbp) of all vascular land plants, and have drought‐resistant resurrection phenotypes that permit survival for months in a desiccated dormant state and the ability to return to full photosynthetic capacity following soil moisture availability. With interest in the ecological and evolutionary importance of their resurrection phenotypes, and taking advantage of the small genome sizes in Selaginella, we generated high coverage PacBio (~80x), and paired‐end and mate‐pair Illumina libraries (~140x). We then performed a hybrid PacBio‐Illumina assembly to generate a de novo assembly for the resurrection fern Selaginella arizonica. We present our de novo draft genome of S. arizonica and highlight genomic attributes associated with the resurrection phenotype. 56
Page 1 and 2:
Sequencing, Finishing, Analysis in
Page 3 and 4:
11th Annual Sequencing, Finishing,
Page 5 and 6: xGen ® Exome Research Panel • Re
Page 7 and 8: 11th Annual Sequencing, Finishing,
Page 55: 11th Annual Sequencing, Finishing,
Page 107 and 108:
Page 109 and 110:
Page 111 and 112:
Page 113 and 114:
Page 115 and 116:
Page 117 and 118:
Page 119 and 120:
Page 121 and 122:
Page 123 and 124:
Page 125 and 126:
Page 127 and 128:
Page 129 and 130:
Page 131 and 132:
Page 133 and 134:
Page 135 and 136:
Page 137 and 138:
Page 139 and 140:
Page 141 and 142:
Page 143 and 144:
Page 145 and 146:
Page 147 and 148:
Page 149 and 150:
Page 151 and 152:
Page 153 and 154:
Page 155 and 156:
Page 157 and 158:
Page 159 and 160:
Page 161 and 162:
Reliable solutions for focused NGS
Page 163 and 164:
Page 165 and 166:
Page 167:
166
show all

Sequencing

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?