Background . Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including ( i ) read pre-processing and metagenome assembly, ( ii ) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and ( iii ) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results. Tools specifically designed for metagenomes, specifically metaSPAdes and MEGAHIT, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5x coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥ 97%) and when the most abundant strain represented < 50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: ( i ) ≥ 10kb contig lengths to define populations, ( ii ) coverage defined from reads mapping at ≥ 90% identity, and ( ii ) ≥ 75% of contig length with ≥ 1x coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. Conclusions. These simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.

We present the transient source detection efficiencies of the Palomar Transient Factory (PTF), parameterizing the number of transients that PTF found versus the number of similar transients that occurred over the same period in the survey search area but were missed. PTF was an optical sky survey carried out with the Palomar 48 inch telescope over 2009-2012, observing more than 8000 square degrees of sky with cadences of between one and five days, locating around 50,000 non-moving transient sources, and spectroscopically confirming around 1900 supernovae. We assess the effectiveness with which PTF detected transient sources, by inserting ≃7 million artificial point sources into real PTF data. We then study the efficiency with which the PTF real-time pipeline recovered these sources as a function of the source magnitude, host galaxy surface brightness, and various observing conditions (using proxies for seeing, sky brightness, and transparency). The product of this study is a multi-dimensional recovery efficiency grid appropriate for the range of observing conditions that PTF experienced and that can then be used for studies of the rates, environments, and luminosity functions of different transient types using detailed Monte Carlo simulations. We illustrate the technique using the observationally well-understood class of type Ia supernovae.

We present an optical nebular spectrum of the nearby Type Ia supernova 2011fe, obtained 981 d after explosion. SN 2011fe exhibits little evolution since the +593 d optical spectrum, but there are several curious aspects in this new extremely late-time regime. We suggest that the persistence of the ~5800 Å feature is due to Na I D, and that a new emission feature at ~7300 Å may be [Ca II]. Also, we discuss whether the new emission feature at ~6400 Å might be [Fe I] or the high-velocity hydrogen predicted by Mazzali et al. The nebular feature at 5200 Å exhibits a linear velocity evolution of ~350 km s-1 per 100 d from at least +220 to +980 d, but the line's shape also changes in this time, suggesting that line blending contributes to the evolution. At ~1000 d after explosion, flux from the SN has declined to a point where contribution from a luminous secondary could be detected. In this work, we make the first observational tests for a post-impact remnant star and constrain its temperature and luminosity to T ≳ 104 K and L ≲ 104 L⊙. Additionally, we do not see any evidence for narrow H α emission in our spectrum. We conclude that observations continue to strongly exclude many single-degenerate scenarios for SN 2011fe.

We analyse spectroscopic measurements of 122 Type Ia supernovae (SNe Ia) with z < 0.09 discovered by the Palomar Transient Factory, focusing on the properties of the Si II λ6355 and Ca ii 'near-infrared triplet' absorptions. We examine the velocities of the photospheric Si II λ6355, and the velocities and strengths of the photospheric and high-velocity Ca II, in the context of the stellar mass (Mstellar) and star formation rate (SFR) of the SN host galaxies, as well as the position of the SN within its host. We find that SNe Ia with faster Si II λ6355 tend to explode in more massive galaxies, with the highest velocity events only occurring in galaxies with Mstellar > 3 × 109 M⊙. We also find some evidence that these highest velocity SNe Ia explode in the inner regions of their host galaxies, similar to the study of Wang et al., although the trend is not as significant in our data. We show that these trends are consistent with some SN Ia spectral models, if the host galaxy stellar mass is interpreted as a proxy for host galaxy metallicity. We study the strength of the high-velocity component of the Ca II near-IR absorption, and show that SNe Ia with stronger high-velocity components relative to photospheric components are hosted by galaxies with low Mstellar, blue colour, and a high sSFR. Such SNe are therefore likely to arise from the youngest progenitor systems. This argues against a pure orientation effect being responsible for high-velocity features in SN Ia spectra and, when combined with other studies, is consistent with a scenario where high-velocity features are related to an interaction between the SN ejecta and circumstellar medium local to the SN.