Improving draft genome contiguity with reference-derived in silico mate-pair libraries
نویسندگان
چکیده
منابع مشابه
Genome scaffolding with PE-contaminated mate-pair libraries
Scaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-ends libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problem is so-called PE-contamination in mate-pair libraries, in which a non-negligible f...
متن کاملTheoretical Bounds on Mate-Pair Information for Accurate Genome Assembly
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome reconstruction is NP-hard when framed as finding the shortest sequence that contains all observed reads. Although this original formulation is very simplistic and doe...
متن کاملTranscriptome Sequencing of Guilan Native Cow in Comparison with bosTau4 Reference Genome
RNA-sequencing is a new method of transcriptome characterization of organisms. Based on identity and relatedness, there are large genetic variations among different cattle breeds. The goal of the current study was to sequence the transcriptome of Guilan native cow and compare with available reference genome using RNA-sequencing method. Blood samples were collected from 14 Guilan native cows and...
متن کاملSequencing and Assembly of the 22-Gb Loblolly Pine Genome
Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun...
متن کاملNextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
SUMMARY Illumina's recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to maximize their value, post-sequencing ...
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: GigaScience
سال: 2018
ISSN: 2047-217X
DOI: 10.1093/gigascience/giy029