Tools
Sorted by:
Try your query at:
 |
 |
 |
 |
 |
 |
Results 1 - 10
of
25
Genome analysis Consensus generation and variant detection by Celera Assembler
"... Motivation: We present an algorithm to identify allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences, and to produce a set of haploid consensus sequences rather than a single consensus sequence. Existing WGS assemblers take a column-by-column approach to consensus gener ..."
Abstract
- Add to MetaCart
of sequence variation. In 33 269 out of 460 373 detected regions of size 41 bp, it fixes the constructed errors of a mosaic haploid representation of a diploid locus as produced by the original Celera Assembler consensus algorithm. Using an optimized procedure calibrated against 1 506 344 known SNPs
The diploid genome sequence of an individual human
- PLoS Biol
"... Presented here is a genome sequence of an individual human. It was produced from;32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given r ..."
Abstract
-
Cited by 293 (6 self)
- Add to MetaCart
region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4
Improving Genome Assembly without Sequencing
"... Assembly of genomes from whole-genome sequencing (WGS) projects is one of the most complex computational problems in genomics. WGS assemblers such as Arachne [1] and Celera Assembler [2] are able to process data from millions of individual sequence "reads " and construct an accurat ..."
Abstract
- Add to MetaCart
Assembly of genomes from whole-genome sequencing (WGS) projects is one of the most complex computational problems in genomics. WGS assemblers such as Arachne [1] and Celera Assembler [2] are able to process data from millions of individual sequence "reads " and construct
Genome analysis Aggressive assembly of pyrosequencing reads with mates
"... Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a ‘hybrid ’ approach to whole-genome shotgun sequencing projects, b ..."
Abstract
- Add to MetaCart
, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data. Results: Celera Assembler was modified
unknown title
"... holder Ns) that have no BLAST hit at 99 % identity for Þnished data and 95 % identity for light-shotgun data were considered uncovered. The percentage of each clone not hit by Celera sequence was calculated by dividing the total length of the uncovered sequence by the sequence length of the clone. T ..."
Abstract
- Add to MetaCart
. The total number of nucleotides that have no coverage in the Celera assem-bled contigs was calculated by summing the regions of no hits for all the clones that covered Celera contigs by less than 90 % (95 % for Þnished clones). This cutoff value was chosen to eliminate the occasionally low quality
The greedy path-merging algorithm for sequence assembly
- Proc. RECOMB 2001
, 2001
"... Two different approaches to determining the human genome are currently being pursued: one is the “clone-by-clone ” approach, employed by the publicly-funded Human Genome Project, and the other is the “whole genome shotgun ” approach, favored by researchers at Celera Genomics. An interim strategy emp ..."
Abstract
-
Cited by 9 (3 self)
- Add to MetaCart
employed at Celera, called compartmentalized assembly, makes use of preliminary data produced by both approaches. This paper introduces the Bactig Ordering Problem, which is a key problem that arises in this context, and presents an efficient heuristic called the greedy path-merging algorithm that performs
RESEARCH ARTICLE Open Access
"... Background: Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targe ..."
Abstract
- Add to MetaCart
was implemented within the Celera Assembler software and its pyrosequencing-specific variant, CABOG. The implementation was tested on Sanger and pyrosequencing data from six genomes. The bounding read assemblies were compared to assemblies from two other methods on the same data. The algorithm generates improved
A preprocessor for shotgun assembly of large genomes
- Journal of Computational Biology
, 2004
"... The whole-genome shotgun (WGS) assembly technique has been remarkably successful in efforts to determine the sequence of bases that make up a genome. WGS assembly begins with a large collection of short fragments that have been selected at random from a genome. The sequence of bases at each end of t ..."
Abstract
-
Cited by 6 (2 self)
- Add to MetaCart
collectively the “UMD Overlapper”, can be run iteratively and as a preprocessor for other assemblers. We tested the UMD Overlapper on Celera’s Drosophila reads. When we replaced Celera’s overlap procedures in the front end of their assembler, it was able to produce a significantly improved genome.
Genome-Wide DNA Alignment Similarity (Identity) for 40,000 Chimpanzee DNA Sequences Queried against the
"... To provide a fresh and less-biased global set of analyses, large-scale comparative DNA sequence alignments between the chimpanzee and human genomes were performed with the BLASTN algorithm. One group of experiments was conducted with query and subject low-complexity sequence masking enabled while th ..."
Abstract
- Add to MetaCart
each involved a data set of 40,000 chimpanzee whole genome shotgun sequences (WGSS) obtained from the National Center for Biotechnology (NCBI) and queried against four different human genome assemblies (GRCH37, GRCH36, Alternate SNP Assembly, and the Celera Assembly). The use of low complexity sequence
Shotgun Assembler Profiling and Benchmark Development
"... Abstract — The output quality of assemblers has been under scrutiny [1] due to presence of misassembles in many draft genomes. The assembly quality parameters cited are often not true indicators of a correct assembly and are sensitive to input parameters and genome structure. This paper presents a e ..."
Abstract
- Add to MetaCart
, repeat length, repeat frequency etc. We experiment with 4 assemblers MIRA [2], Celera WGS [3], Velvet [4] and EulerSR [5]. The first 2 prescribe to the overlap layout consensus (OLC) model [6] and the latter to the de-Brujin Graph model[7]. In this work we use synthetic and actual shotgun reads
Results 1 - 10
of
25
