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Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data alone, particularly with highly repetitive plant genomes. Errors in the raw data...
The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from th...
Let D = (V (D), A(D)) be a digraph and k ≥ 2 an integer. We say that D is k-quasi-transitive if for every directed path (v0, v1, . . . , vk) in D, then (v0, vk) ∈ A(D) or (vk, v0) ∈ A(D). Clearly, a 2-quasi-transitive digraph is a quasi-transitive digraph in the usual sense. Bang-Jensen and Gutin proved that a quasi-transitive digraph D has a 3king if and only if D has a unique initial strong c...
MOTIVATION Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are charac...
between two reads indicates an approximate overlap between the reads. Since the algorithm finds approximate overlaps directly, it can process reads without errorcorrection preprocessing steps. Extensions of the algorithm, such as construction graphs of overlapping pairs of reads, are discussed. The algorithm can be used to construct graphs for assembly and for other related applications such as...
New short-read sequencing technologies produce large volumes of 25-30 base paired-end reads. In this paper, we present a sequencing protocol and de novo assembler program (SHORTY) targeted towards such microread data. Our protocol augments short-paired reads using a trivially small number of Sanger reads (only one to three reads per bacterial genome). Still, these “seed reads” enable us to prod...
This article examines the production of prose texts in pre-Alfredian England. After reviewing conventional ideas regarding foundational role assigned to Alfred, king Wessex, creation Old English genre, discussion turns a quite considerable number non-poetic which were demonstrably produced at an earlier time, asking whether these can be regarded as prose. Following investigation medieval and mo...
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