Sequence assembly with CAFTOOLS.
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/.
Dear
S
S
Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Durbin
R
R
Hillier
L
L
Marth
G
G
Thierry-Mieg
J
J
Mott
R
R
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D015723:Gene Library; D016678:Genome; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*