Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads
نویسندگان
چکیده
منابع مشابه
HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads
BACKGROUND AND OBJECTIVE Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. METHODS We developed Hierarchical mUlti-refere...
متن کاملSlideSort: all pairs similarity search for short reads
MOTIVATION Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses. RESULTS In this study, we designed and implemented an exact algorithm SlideSor...
متن کاملA Mathematician Reads
New York University mathematical physicist Alan Sokal published in the postmodern humanities journal Social Text a parody entitled “Transgressing the Boundaries: Toward a Transformative Hermeneutics of Quantum Gravity” [1]. His point in doing so was to test whether the field of “cultural studies of science” was seriously lacking in “intellectual standards”. His article is nonsense from start to...
متن کاملDisk Reads with DRAM Latency
The gap between the access time of primary and secondary storage technologies, often called the access gap, has long constrained the performance of computer systems. Unfortunately, this gap is growing, not shrinking. While today’s technologies improve the capacity of both of these storage media at a furious pace, they are not as successful at reducing access times. Instead, the speed of computa...
متن کاملImportant biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq)
Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigate...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: F1000Research
سال: 2019
ISSN: 2046-1402
DOI: 10.12688/f1000research.19426.1