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Authors: Benjamin Bolduc, Simon Roux
Group: Sullivan Lab, iVirus
Summary: Cluster genomes is script that clusters genomes at a set nucleotide identity and coverage length. Additonally, it offers the ability to cluster sequences whose ends may not align correspondingly, i.e. the special cases of assembled, circular viral genomes that are treated as 'linear' by other sequence-clustering software (that can "miss" the ends).This is 'beta-like' software that has been vetted, though has not been as thoroughly tested as other widely-recognized clustering tools, such as CD-HIT, UCLUST, etc... As with all software, please examine the final results to see if they make sense.
Proper citation: Benjamin Bolduc, Simon Roux 2017. Clustering Viral Genomes in iVirus. protocols.io dx.doi.org/10.17504/protocols.io.gwebxbe 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. SYBR Gold Working Stock. protocols.io dx.doi.org/10.17504/protocols.io.c82zyd Copy
Authors: Marcia Osburne
Group: VERVE Net, Sullivan Lab
Proper citation: Marcia Osburne 2016. Syn33 g20 PCR. protocols.io dx.doi.org/10.17504/protocols.io.dai2cd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Media Recipes. protocols.io dx.doi.org/10.17504/protocols.io.deq3dv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. DNA Extraction Protocol. protocols.io dx.doi.org/10.17504/protocols.io.c32yqd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is is used with Cesium Chloride Dialysis for Viruses
Proper citation: Matthew Sullivan 2016. MTN100 with 1x NaCl. protocols.io dx.doi.org/10.17504/protocols.io.def3bm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used for the DNA Extraction Protocol.
Proper citation: Matthew Sullivan 2016. CsCl purified phage lysate, Proteinase K, SDS. protocols.io dx.doi.org/10.17504/protocols.io.c68zhv Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: Mapping metagenomic reads from Ocean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter.
Proper citation: Benjamin Bolduc 2016. Mapping Metagenomic Reads to Reference Sequences (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.eyibfue 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.
Proper citation: Benjamin Bolduc 2016. Processing a Viral Metagenome Using iVirus. protocols.io dx.doi.org/10.17504/protocols.io.ev3be8n Copy
Authors: Gary Trubl, Natalie Solonenko, Yueh-Fen Li
Group: Sullivan Lab
Summary: Protocol for resuspending viruses from soils and sediments. See attached file for considerations, adaptations, and references. This version does not include CsCl purification, see version 2 for CsCl information.
Proper citation: Gary Trubl, Natalie Solonenko, Yueh-Fen Li 2018. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io dx.doi.org/10.17504/protocols.io.tzzep76 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Screening Recombinant Clones by PCR. protocols.io dx.doi.org/10.17504/protocols.io.c48yzv Copy
Authors: Shalaja Srinagesh et al
Group: VERVE Net, Sullivan Lab
Proper citation: Shalaja Srinagesh et al 2016. Zobell Agar/Broth Medium. protocols.io dx.doi.org/10.17504/protocols.io.dbn2md Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. One-step growth curves for Cellulophaga phages. protocols.io dx.doi.org/10.17504/protocols.io.ddh235 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is is used with Cesium Chloride Dialysis for Viruses
Proper citation: Matthew Sullivan 2016. MTN100 with 3x NaCl. protocols.io dx.doi.org/10.17504/protocols.io.dee3bd Copy
Authors: Natalie Solonenko
Group: Sullivan Lab
Proper citation: Natalie Solonenko 2020. Ampure bead clean up for high molecular weight DNA . protocols.io dx.doi.org/10.17504/protocols.io.6kphcvn Copy
Authors: Gary Trubl, Natalie Solonenko
Group: Sullivan Lab
Summary: Resuspend viruses from soils and sediments
Proper citation: Gary Trubl, Natalie Solonenko 2017. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io dx.doi.org/10.17504/protocols.io.hu3b6yn Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan Lab 2016. Double SPRI for Second Generation Sequencing. protocols.io dx.doi.org/10.17504/protocols.io.c53y8m Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The following are media recipes necessary for isolating and maintaining Synechococcus isolates.
Proper citation: Matthew Sullivan 2016. Media recipes for Synechococcus isolates. protocols.io dx.doi.org/10.17504/protocols.io.c9jz4m Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. One-Step Growth Curves for Cyanophages. protocols.io dx.doi.org/10.17504/protocols.io.dan2dd Copy
Authors: Li Deng, Bonnie T. Poulos, Matthew B. Sullivan
Group: VERVE Net, Sullivan Lab
Summary: AbstractOcean viruses are abundant, ubiquitous, and play important roles in global biogeochemical cycles through mortality, horizontal gene transfer and manipulation of host metabolism. However, the ability to link viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. Here, we present viral tagging (VT), a method that combines mixtures of isotope labeled host cells and fluorescent viruses with flow cytometry. In a single experiment, we can screen 107 uncultivated ocean viruses with a single strain of Synechococcus. These viruses can then be sequenced to quantitatively link objectivelydefined environmental viral populations, and their genomes, to their hosts.
Proper citation: Li Deng, Bonnie T. Poulos, Matthew B. Sullivan 2016. Obtaining targeted metagenomes from uncultivated environmental Synechococcus using flow cytometry-based viral tagging. protocols.io dx.doi.org/10.17504/protocols.io.c6zzf5 Copy
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