Literature DB >> 9521929

Sequence assembly with CAFTOOLS.

S Dear1, R Durbin, L Hillier, G Marth, J Thierry-Mieg, R Mott.   

Abstract

Large-scale genomic sequencing requires a software infrastructure to support and integrate applications that are not directly compatible. We describe a suite of software tools built around the Common Assembly Format (CAF), a comprehensive representation of a sequence assembly as a text file. These tools form the backbone of sequencing informatics at the Sanger Centre and the Genome Sequencing Center. The CAF format is intentionally flexible, and our Perl and C libraries, which parse and manipulate it, provide powerful tools for creating new applications as well as wrappers to incorporate other software. The tools are available free by anonymous FTP from ftp://ftp.sanger.ac.uk/pub/badger/.

Entities:  

Mesh：

Year:  1998        PMID： 9521929      PMCID： PMC310697          DOI： 10.1101/gr.8.3.260

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  7 in total

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Authors:  S Dear; R Staden
Journal:  DNA Seq       Date:  1992

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Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

3.  Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors:  B Ewing; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

4.  Trace alignment and some of its applications.

Authors:  R Mott
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

5.  Consed: a graphical tool for sequence finishing.

Authors:  D Gordon; C Abajian; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

6.  Experiment files and their application during large-scale sequencing projects.

Authors:  J K Bonfield; R Staden
Journal:  DNA Seq       Date:  1996

7.  A new DNA sequence assembly program.

Authors:  J K Bonfield; K f Smith; R Staden
Journal:  Nucleic Acids Res       Date:  1995-12-25       Impact factor: 16.971
  7 in total
  4 in total

1.  Gene discovery and gene function assignment in filamentous fungi.

Authors:  L Hamer; K Adachi; M V Montenegro-Chamorro; M M Tanzer; S K Mahanty; C Lo; R W Tarpey; A R Skalchunes; R W Heiniger; S A Frank; B A Darveaux; D J Lampe; T M Slater; L Ramamurthy; T M DeZwaan; G H Nelson; J R Shuster; J Woessner; J E Hamer
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-10       Impact factor: 11.205

2.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.

Authors:  Bastien Chevreux; Thomas Pfisterer; Bernd Drescher; Albert J Driesel; Werner E G Müller; Thomas Wetter; Sándor Suhai
Journal:  Genome Res       Date:  2004-05-12       Impact factor: 9.043

3.  Gap5--editing the billion fragment sequence assembly.

Authors:  James K Bonfield; Andrew Whitwham
Journal:  Bioinformatics       Date:  2010-05-30       Impact factor: 6.937

4.  Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.

Authors:  Matthew T G Holden; Heidi Hauser; Mandy Sanders; Thi Hoa Ngo; Inna Cherevach; Ann Cronin; Ian Goodhead; Karen Mungall; Michael A Quail; Claire Price; Ester Rabbinowitsch; Sarah Sharp; Nicholas J Croucher; Tran Bich Chieu; Nguyen Thi Hoang Mai; To Song Diep; Nguyen Tran Chinh; Michael Kehoe; James A Leigh; Philip N Ward; Christopher G Dowson; Adrian M Whatmore; Neil Chanter; Pernille Iversen; Marcelo Gottschalk; Josh D Slater; Hilde E Smith; Brian G Spratt; Jianguo Xu; Changyun Ye; Stephen Bentley; Barclay G Barrell; Constance Schultsz; Duncan J Maskell; Julian Parkhill
Journal:  PLoS One       Date:  2009-07-15       Impact factor: 3.240
  4 in total

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