Shotgun sequencing is the most powerful strategy for large scale sequencing. Two main approaches exist: clone-by-clone and whole genome shotgun (WGS). In the clone-by-clone strategy, overlapping clones are amplified and then sheared in a random fashion. In the WGS approach, a sufficient amount of cells from the target organism are obtained, and the random shearing is performed on extracted DNA....

Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemi...

Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...

MOTIVATION Eugene Myers in his string graph paper suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (...

In a recent work, Mossel and Ross considered the shotgun assembly problem for a random jigsaw puzzle. Their model consists of a puzzle an n×n grid, where each vertex is viewed as a center of a piece. They assume that each of the four edges adjacent to a vertex, is assigned one of q colors (corresponding to ”jigs”, or cut shapes) uniformly at random. Mossel and Ross asked: how large should q = q...

Full-length de novo sequencing from tandem mass (MS/MS) spectra of unknown proteins such as antibodies or proteins from organisms with unsequenced genomes remains a challenging open problem. Conventional algorithms designed to individually sequence each MS/MS spectrum are limited by incomplete peptide fragmentation or low signal to noise ratios and tend to result in short de novo sequences at l...

In recent work by Mossel and Ross, it was asked how large q has to be for a random jigsaw puzzle with q different shapes of “jigs” to have exactly one solution. The jigs are assumed symmetric in the sense that two jigs of the same type always fit together. They showed that for q = o(n) there are a.a.s. multiple solutions, and for q = ω(n) there is a.a.s. exactly one. The latter bound has since ...