This track is part of the Read Coverage collection of the zebra finch telomere-to-telomere hub.
PacBio HiFi reads are long reads with per-base accuracy comparable to short reads, and they are the backbone of this assembly. This track shows how deeply HiFi reads cover each position of the assembly. Flat coverage at the expected depth is the ordinary case; a collapse to zero or a doubling of depth points at an assembly problem or at a repeat that has not been separated correctly.
A bar graph of read depth, autoscaled to the data in view.
A total of 134.3 Gbp of PacBio HiFi data was generated from four sequencing runs of a single library, 7.5 million reads with an N50 of 18,348 bp. Reads were mapped to the diploid assembly and depth was summarized in fixed windows. The coverage tracks were used during manual curation of the assembly graph, which is described in the manuscript.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/assembly_verkko_0.1/manual_curation/bTaeGut7v0.4/mapping/v0.4_dip_hifi/v0.4_dip_hifi.pri.cov.wig. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The conversion, and the whole hub, is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC kent source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=covHifi.
For automated download and analysis, this annotation is a bigWig file inside the hub. Individual regions or the whole annotation can be obtained with bigWigToBedGraph, which can be compiled from source or downloaded as a precompiled binary; instructions are here. The tool also fetches a range, for example bigWigToBedGraph <hubUrl>/GCF_048771995.1/covHifi.bw -chrom=NC_133024.1 -start=0 -end=100000 stdout, where <hubUrl> is the directory this hub was loaded from.
The original annotation files are on GenomeArk, in the bTaeGut7 annotations directory.
Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, Chen Y et al. The complete genome of a songbird. Cell. 2026 Aug 6;189(16):4922-4945.e12. PMID: 42561917
The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before and after publication. The analysis code is at github.com/gf777/T2T-zebra-finch. This hub was assembled at UCSC from the IGV session distributed with the annotations, using hubtools.