PCAP: a whole-genome assembly program.

By Xiaoqiu Huang, Jianmin Wang, Srinivas Aluru, Shiaw-Pyng Yang, LaDeana W. Hillier. Genome Research, 2003

322 citations recorded by the source corpus.

We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis of many overlaps with other reads, instead of many shorter word matches with other reads. Contaminated end regions of reads are identified and removed. Generation of a consensus sequence for a contig is based on an alignment of reads in the contig, in which both base quality values and coverage information are used to determine every consensus base. The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0ddc53f698d85b9050bbff0f12c1f6894b405562

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Citations in the corpus

Evolution of Symbiotic Bacteria in the Distal Human Intestine (2007, methodology): “Genome sequencing. The B. vulgatus and B. distasonis genomes were assembled from two types of whole-genome shotgun libraries: a plasmid library with an average insert size of 5 Kb, and a fosmid library with an average insert size of 40 Kb. For each genome, both Phrap (http://www.phrap.org/) and PCAP”
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans (2007, methodology): “A D. yakuba strain Tai18E2 wholegenome shotgun assembly (v2.0; http://genome.wustl.edu/) generated by the Parallel Contig Assembly Program (PCAP) [ 18 ] was aligned to the D. melanogaster reference sequence (Materials and Methods).”
De novo fragment assembly with short mate-paired reads: Does the read length matter? (2009, background): “Most de novo assemblers for Sanger reads follow the “overlap-layout-consensus” paradigm that is optimized for such reads [13, 15] and does not scale well for short read assembly.”
The fragment assembly string graph (2005, background): “…capable of wholegenome assembly that all perform comparably by employing variations on the basic paradigm of first finding and assembling unique stretches of DNA with high reliability (Myers et al., 2000; Aparicio et al., 2002; Mullikin and Ning, 2003; Jaffe et al., 2003; Huang et al., 2003).”
Assembly of large genomes using second-generation sequencing. (2010, background): “Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads.”
The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol (2012, methodology): “Reads were trimmed to remove low quality bases and to remove the first 11 bases corresponding to the primer region by a script based on Trim2 [54,55]), and then the reads were separated by barcode [56]).”
High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples (2012, methodology): “Assembly was first conducted by PCAP [47], which enabled parallelized rapid assembling, with a sequence identity setting of 92%.”
Short read fragment assembly of bacterial genomes. (2008, methodology): “…Pevzner et al. (1989) described a simple algorithm for constructing the SBH repeat graph, it is not immediately clear how to generalize the approaches in the studies by Huang et al. (2003) and Jaffe et al. (2003) for efficient construction of the repeat graph even in the simple case of SBH " reads.”
Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment (2014, methodology): “Reads were trimmed to remove low-quality bases and to remove the first 11 bases corresponding to the primer region, by a script based on Trim2 [19].”
The MaSuRCA genome assembler (2013, methodology): “, 2008), PCAP (Huang, 2003), Arachne (Batzoglou et al.”
De novo assembly of human genomes with massively parallel short read sequencing. (2010, methodology): “Several programs, such as phrap (http://www.phrap.org), Celera assembler (Myers et al. 2000), ARACHNE (Batzoglou et al. 2002), Phusion (Mullikin and Ning 2003), RePS (Wang et al. 2002), PCAP (Huang et al. 2003), and Atlas (Havlak et al. 2004), have been successfully used for de novo assembly of whol”