arXiv subjects

Haowen Zhang

Publications and source records attributed to Haowen Zhang.

40 records · Page 3Linked to original sources

arXiv2020

Haplotype-resolved de novo assembly with phased assembly graphs

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a new de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five non-human datasets, including California redwood with a $\sim$30-gigabase hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

q-bio.GN↗

arXiv2019

Can intrinsic alignments of elongated low-mass galaxies be used to map the cosmic web at high redshift?

Hubble Space Telescope observations show that low-mass ($M_*=10^9-10^{10}M_{\odot}$) galaxies at high redshift ($z=1.0-2.5$) tend to be elongated (prolate) rather than disky (oblate) or spheroidal. This is explained in zoom-in cosmological hydrodynamical simulations by the fact that these galaxies are forming in cosmic web filaments where accretion happens preferentially along the direction of elongation. We ask whether the elongated morphology of these galaxies allows them to be used as effective tracers of cosmic web filaments at high redshift via their intrinsic alignments. Using mock lightcones and spectroscopically-confirmed galaxy pairs from the CANDELS survey, we test two types of alignments: (1) between the galaxy major axis and the direction to nearby galaxies of any mass, and (2) between the major axes of nearby pairs of low-mass, likely prolate, galaxies. The mock lightcones predict strong signals in 3D real space, 3D redshift space, and 2D projected redshift space for both types of alignments (assuming prolate galaxy orientations are the same as those of their host prolate halos), but we do not detect significant alignment signals in CANDELS observations. However, we show that spectroscopic redshifts have been obtained for only a small fraction of highly elongated galaxies, and accounting for spectroscopic incompleteness and redshift errors significantly degrades the 2D mock signal. This may partly explain the alignment discrepancy and highlights one of several avenues for future work.

astro-ph.GA↗

arXiv2018

The evolution of galaxy shapes in CANDELS: from prolate to oblate

We model the projected b/a-log a distributions of CANDELS main sequence star-forming galaxies, where a (b) is the semi-major (semi-minor) axis of the galaxy images. We find that smaller-a galaxies are rounder at all stellar masses M and redshifts, so we include a when analyzing b/a distributions. Approximating intrinsic shapes of the galaxies as triaxial ellipsoids and assuming a multivariate normal distribution of galaxy size and two shape parameters, we construct their intrinsic shape and size distributions to obtain the fractions of prolate, oblate and spheroidal galaxies in each redshift and mass bin. We find that galaxies tend to be prolate at low m and high redshifts, and oblate at high M and low redshifts, qualitatively consistent with van der Wel et al. (2014), implying that galaxies tend to evolve from prolate to oblate. These results are consistent with the predictions from simulations (Ceverino et al. 2015, Tomassetti et al. 2016) that the transition from prolate to oblate is caused by a compaction event at a characteristic mass range, making the galaxy center baryon dominated. We give probabilities of a galaxy's being prolate, oblate or spheroidal as a function of its M, redshift, projected b/a and a, which can facilitate target selections of galaxies with specific shapes at hight redshifts. We also give predicted optical depths of galaxies, which are qualitatively consistent with the expected correlation that AV should be higher for edge-on disk galaxies in each log a slice at low redshift and high mass bins.

astro-ph.GA↗

arXiv2017

Broadband Photometric Reverberation Mapping Analysis on SDSS-RM and Stripe 82 Quasars

We modified the broadband photometric reverberation mapping (PRM) code, JAVELIN, and tested the availability to get broad line region (BLR) time delays that are consistent with the spectroscopic reverberation mapping (SRM) project SDSS-RM. The broadband light curves of SDSS-RM quasars produced by convolution with the system trans- mission curves were used in the test. We found that under similar sampling conditions (evenly and frequently sampled), the key factor determining whether the broadband PRM code can yield lags consistent with the SRM project is the flux ratio of the broad emission line to the reference continuum, which is in line with the previous findings. We further found a critical line-to-continuum flux ratio, about 6%, above which the mean of the ratios between the lags from PRM and SRM becomes closer to unity, and the scatter is pronouncedly reduced. We also tested our code on a subset of SDSS Stripe 82 quasars, and found that our program tends to give biased lag estimations due to the observation gaps when the R-L relation prior in Markov Chain Monte Carlo (MCMC) is discarded. The performance of the damped random walk (DRW) model and the power-law (PL) structure function model on broadband PRM were compared. We found that given both SDSS-RM-like or Stripe 82-like light curves, the DRW model performs better in carrying out broadband PRM than the PL model.

astro-ph.GA↗