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Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: PCPipe is a protein-clustering tool.  The input is a set of ORFs and a FASTA file with already clustered ORFs. The process entails:Use cd-hit-2d to compare the input peptides to previously clustered proteinsThe result is a file with input proteins that clustered to existing clusters and those that did notUse the unclustered peptides and self-cluster them via cd-hitTake a representative sequence from each novel cluster, and use "blastp" to compare to SIMAP.Use the resulting SIMAP "feature_id" to look up the SIMAP features, merging the query results with the protein ID into a tab-delimited annotations fileProvide the user with two cluster files and the annotations for the new clusters based on the representative sequenceCode is freely available at Github.

Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. PCPipe: Protein clustering with SIMAP annotations. protocols.io https://dx.doi.org/10.17504/protocols.io.ehfbb3n Copy   

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Authors: SangHoon Lee
Group: VERVE Net, Fuhrman Lab
Summary: Filtering protocol adapted from SangHoon Lee

Proper citation: SangHoon Lee 2015. Filtering for Cell Collection. protocols.io https://dx.doi.org/10.17504/protocols.io.dmb42m Copy   

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Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab
Summary: Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome.Methods:We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome.

Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Installation and Getting Started. protocols.io https://dx.doi.org/10.17504/protocols.io.d5k84v Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Chlorovirus Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.er2bd8e Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: From Sullivan M., Lindell D., Lee J., Thompson L., Bielawski J., Chisholm S. Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts.PLOS Biology, 2006 4(8):e234. Please see the published manuscript for additional information.

Proper citation: Matthew Sullivan 2016. Amplification of phage genes from lysates and environmental samples. protocols.io https://dx.doi.org/10.17504/protocols.io.djn4md Copy   

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Authors: Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen
Group: VERVE Net
Summary: This protocol is from:Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB (2008) Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation. PLoS Genet 4(6): e1000106. doi:10.1371/journal.pgen.1000106Please see the full manuscript for additional details.(Image: calf, Jim Champion, CC BY-SA)

Proper citation: Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen 2015. Eisen Lab, Fresh Cow Dung. protocols.io https://dx.doi.org/10.17504/protocols.io.ebebaje Copy   

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Authors: DeLong Lab
Group: VERVE Net, Sullivan Lab

Proper citation: DeLong Lab 2015. Lysozyme & RNase A Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dje4jd Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan Lab 2016. Preparation of Virus DNA from Seawater for Metagenomics. protocols.io https://dx.doi.org/10.17504/protocols.io.c28yhv Copy   

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Authors: Karen D. Weynberg, Elisha M. Wood-Charlson, Curtis A. Suttle, and Madeleine J. H. van Oppen
Group: VERVE Net
Summary: For use in Generating viral metagenomes from the coral holobiont.

Proper citation: Karen D. Weynberg, Elisha M. Wood-Charlson, Curtis A. Suttle, and Madeleine J. H. van Oppen 2016. 9 ?L reaction mix. protocols.io https://dx.doi.org/10.17504/protocols.io.emcbc2w Copy   

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Authors: Steven Wilhelm
Group: VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Adapted from: Van Etten, J. (n.d.). Titering of Chlorella Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/

Proper citation: Steven Wilhelm 2016. Virus Purification by Sucrose Density Gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.grzbv76 Copy   

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Authors: Kristin Corrier/Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: For use in 'FASP Kit Protocol-ORNL Developed for Bacteriophage'

Proper citation: Kristin Corrier/Nathan VerBerkmoes 2016. Urea Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dei3cd Copy   

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Authors: Jozef Nissimov
Group: VERVE Net, Bidle Lab
Summary: Concentrating Viruses via PEG precipitation

Proper citation: Jozef Nissimov 2015. Concentrating Viruses via PEG precipitation. protocols.io https://dx.doi.org/10.17504/protocols.io.d9j94m Copy   

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Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: The following continued adaptation of Hennes et al. (1995) is a result of FLVP assay optimizations for the Vibrio alginolyticus PWH3a-phage P1 phage-host system (PHS) for use with SYBR Green I stain. Novices to microscopy would benefit from reading Wen et al. (2004) for details on preparing and storing slides using SYBR Green I stain. This protocol is a modification of the standard slide preparation techniques for bacteria and viruses in aquatic samples (see Suttle and Fuhrman 2010, this volume).

Proper citation: André M. Comeau and Rachel T. Noble 2016. FLVP assays. protocols.io https://dx.doi.org/10.17504/protocols.io.dzr755 Copy   

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Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: Comeau, A. M., and R. T. Noble. 2010. Preparation and application of fluorescently labeled virus particles, p. 19–29. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.Please see the published manuscript for additional information.

Proper citation: André M. Comeau and Rachel T. Noble 2016. Preparation and application of fluorescently labeled virus particles. protocols.io https://dx.doi.org/10.17504/protocols.io.d2q8dv Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: .

Proper citation: Matthew Sullivan 2016. 0.7% Agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.c7bzim Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Cellulophaga Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.dez3f5 Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Buffer C. protocols.io https://dx.doi.org/10.17504/protocols.io.esybefw Copy   

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Authors: Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: Collaborator, Nathan VerBerkmoes (Oak Ridge National Labs), worked with Tucson Marine Phage Lab to develop more sensitive proteomics assays for viral isolates which we are now also using for environmental viral concentrates. A new sample prep method (FASP) was optimized to maximize the signal from our commonly low-protein containing samples, and then run using 2d-LC-MS-MS to maximize detection across the large dynamic range in isolate and environmental samples.

Proper citation: Nathan VerBerkmoes 2016. FASP Kit Protocol-ORNL Developed for Bacteriophage. protocols.io https://dx.doi.org/10.17504/protocols.io.ddn25d Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Silver Development protocol (silver stain) for 0.75mm polyacrylamide gels. protocols.io https://dx.doi.org/10.17504/protocols.io.ermbd46 Copy   

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Authors: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack
Group: VERVE Net, Hurwitz Lab
Summary: This tutorial explains how to download entire libraries of data from the VIROME web application. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] See site for more information.

Proper citation: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. VIROME: Downloading libraries of VIROME data. protocols.io https://dx.doi.org/10.17504/protocols.io.d5m845 Copy   

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