Literature DB >> 18428744

Generating a genome assembly with PCAP.

Xiaoqiu Huang1, Shiaw-Pyng Yang.   

Abstract

This unit describes how to use the Parallel Contig Assembly Program (PCAP) to assemble the data produced by a whole-genome shotgun sequencing project. We present a basic protocol for using PCAP on a multiprocessor computer in a 300-Mb genome assembly project. A support protocol to prepare input files for PCAP is also described. Another basic protocol for using PCAP on a distributed cluster of computers in a 3-Gb genome assembly project is presented, in addition to suggestions for understanding results from PCAP.

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Year:  2005        PMID： 18428744     DOI： 10.1002/0471250953.bi1103s11

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  7 in total

Review 1.  Assembly algorithms for next-generation sequencing data.

Authors:  Jason R Miller; Sergey Koren; Granger Sutton
Journal:  Genomics       Date:  2010-03-06       Impact factor: 5.736

2.  Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.

Authors:  Ernesto Picardi; David S Horner; Matteo Chiara; Riccardo Schiavon; Giorgio Valle; Graziano Pesole
Journal:  Nucleic Acids Res       Date:  2010-04-12       Impact factor: 16.971

3.  Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes.

Authors:  Changbin Chen; Andrew D Farmer; Raymond J Langley; Joann Mudge; John A Crow; Gregory D May; James Huntley; Alan G Smith; Ernest F Retzel
Journal:  BMC Plant Biol       Date:  2010-12-17       Impact factor: 4.215

4.  Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.

Authors:  Miguel Pignatelli; Andrés Moya
Journal:  PLoS One       Date:  2011-05-23       Impact factor: 3.240

5.  Feature-by-feature--evaluating de novo sequence assembly.

Authors:  Francesco Vezzi; Giuseppe Narzisi; Bud Mishra
Journal:  PLoS One       Date:  2012-02-03       Impact factor: 3.240

6.  Aggressive assembly of pyrosequencing reads with mates.

Authors:  Jason R Miller; Arthur L Delcher; Sergey Koren; Eli Venter; Brian P Walenz; Anushka Brownley; Justin Johnson; Kelvin Li; Clark Mobarry; Granger Sutton
Journal:  Bioinformatics       Date:  2008-10-24       Impact factor: 6.937

Review 7.  Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.

Authors:  Wenming Xiao; Leihong Wu; Gokhan Yavas; Vahan Simonyan; Baitang Ning; Huixiao Hong
Journal:  Pharmaceutics       Date:  2016-04-22       Impact factor: 6.321
  7 in total

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