In Jena, an equimolar pool of 42 UDG-half libraries was prepared for shotgun sequencing on an Illumina HiSeq 4000 platform using a single-end 76-cycle sequencing kit. All of the sequenced libraries showed high human endogenous DNA proportions (Table S1) and ancient DNA characteristic damage pat...
Genome-wide data were generated for 271 ancient individuals using shotgun sequencing. We obtained genome coverages ranging from 0.15- to 7.09-fold, with an average of 1.97-fold, and quality control with MapDamage 2.0,11 Schmutzi,12 and ANGSD13 estimated negligible contamination in nearly all samp...
pestis strain with signatures associated with flea adaptation has been reported during the Iron Age through shotgun sequencing of an ~2900-year-old genome from Armenia (strain RISE397), though at a coverage too low (0.25-fold) to permit confident phylogenetic positioning2. Although the mechanism ...
Both the initial shotgun and target-enriched libraries were single-end sequenced on an Illumina Hiseq 4000 platform (1 × 75 + 8 + 8 cycles). Sequenced reads were demultiplexed allowing one mismatch in each index and further processed using EAGER (v 1.92.54)29. First, adapter...
The 18 alphaproteobacterial genomes were sequenced by whole- genome shotgun sequencing using a combination of 454 pyrose- quencing and Illumina. The status and characteristics of the genomes are listed in Table 1. Increasing the phylogenetic diversity reduced the systematic errors. We asked whether ...
Adopting a whole-genome shotgun sequencing strategy, we generated a total of 520 Gb of clean Illumina reads from libraries with different insert sizes, with estimated genome coverages of around 178-, 229-, 50.8-, and 210-fold for B. amplexicaulis, O. latifolia, G. angustifolia, and R....
Genomic DNAs were isolated from the leaves of semi-wild wheat Zang1817 (Triticum aestivumssp.tibetanumShao) using the modified CTAB40and subjected to libraries construction. Two PCR-free paired-end shotgun libraries were constructed using DNA template size of ~470 bp, and sequenced on the Hi...
we use mapDamage v.2.0.9-dirty84with default parameters. With exception of the individuals with a few HBV reads in shotgun data and those where full-UDG treatment of the libraries was performed for the in-solution capture experiment, all the others show the typical damage patterns of ancient...