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Authors: Benjamin Bolduc
Group: Sullivan Lab
Summary: Assembling actual reads from the Ocean Sampling Day (2014) using SPAdes, an assembler implemented in Cyverse.
Proper citation: Benjamin Bolduc 2016. Assembling Viral Metagenomic Data with SPAdes (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.evzbe76 Copy
Authors: Kristin Corrier/Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: For use in the "FASP Kit Protocol-ORNL Developed for Bacteriophage"
Proper citation: Kristin Corrier/Nathan VerBerkmoes 2016. Digestion Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dek3cv Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: Preparing data for use in vContact by using VirSorted Ocean Sampling Day (2014) contigs, using tools available in Cyverse. This protocol creates a BLAST DB, BLASTs sequences, and creates a gene-to-contig mapping file. Results from this protocol are suitable for vContact-PCs.
Proper citation: Benjamin Bolduc 2016. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eyhbft6 Copy
Authors: DeLong Lab
Group: VERVE Net, Sullivan Lab
Proper citation: DeLong Lab 2015. Proteinase K Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.djf4jm Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.
Proper citation: Benjamin Bolduc 2017. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gwcbxaw Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
Summary: A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.Quality trimming of reads is important!
Proper citation: Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ewbbfan Copy
Authors: Forest Rohwer
Group: VERVE Net, Sullivan Lab
Summary: This protocol is based on RT Noble and JA Fuhrman (1998) Aquatic Microbial Ecology 12:113-118: Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria.
Proper citation: Forest Rohwer 2016. SYBR Green or Gold Staining. protocols.io https://dx.doi.org/10.17504/protocols.io.c7sznd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Can be used for diluting or resuspending phage preparations.
Proper citation: Matthew Sullivan 2015. Phage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5ey3d Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng 2016. WH7803 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dak2cv Copy
Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses
Proper citation: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Ascorbic-EDTA Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c8xzxm Copy
Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab
Proper citation: Natalie Solonenko 2016. One-step growth curves for Pseudoalteromonas phages. protocols.io https://dx.doi.org/10.17504/protocols.io.den3dd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. DNA Precipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c34yqv Copy
Authors: Bertillson et al.
Group: VERVE Net, Sullivan Lab
Summary: Purpose: To test axenic cultures for purity
Proper citation: Bertillson et al. 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.dcm2u5 Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan Lab 2015. 1M Sodium citrate. protocols.io https://dx.doi.org/10.17504/protocols.io.c6azad Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Plaque assay protocol for Cellulophaga. protocols.io https://dx.doi.org/10.17504/protocols.io.ddg23v Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Modified after Glöckner et al. 1999
Proper citation: Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.c3ayid Copy
Authors: Forest Rohwar
Group: VERVE Net, Sullivan Lab
Summary: In tangential flow filtration (TFF), the sample is run parallel to the filter. Particles that are smaller than the pore size are pushed out through the holes (the filtrate). Particles that are larger than the pore size are retained inside the filter (the retentate). TFF is most effective when a reservoir is used so that the sample can be recycled through numerous times.
Proper citation: Forest Rohwar 2016. Phage Tangential Flow Filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.c7yzpv Copy
Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab
Proper citation: Natalie Solonenko 2016. Plaque Assay Protocol for Pseudoalteromonas. protocols.io https://dx.doi.org/10.17504/protocols.io.de33gm Copy
Authors: Marine Phage Lab, Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega.
Proper citation: Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io https://dx.doi.org/10.17504/protocols.io.c26yhd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Pseudoalteromonas Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.de23gd Copy
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