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* IO_LIB package /fs/sz-user-supported/common/packages/io_lib-1.11-x86_64/bin/ | * IO_LIB package /fs/sz-user-supported/common/packages/io_lib-1.11-x86_64/bin/ | ||
* STADEN package /fs/sz-user-supported/common/packages/staden-src-1-7-0/distrib/unix-rel-1-7-0/linux-bin | |||
== Assembly Formats == | == Assembly Formats == | ||
[http://bioportal.cgb.indiana.edu/docs/tools/cap3/aceform ace] | [http://bioportal.cgb.indiana.edu/docs/tools/cap3/aceform ace] | ||
Revision as of 17:05, 30 October 2007
Sanger
454 (single reads)
454 (paired ends)
Features:
* approximately 84-nucleotide DNA fragments * have a ~ 44-mer linker sequence in the middle * flanked by a ~ 20-mer sequence on each side. * The two flanking 20-mers are segments of DNA that were originally located approximately 2.5 kb apart in the genome of interest. * The ordering and orienting of contigs generates scaffolds which provide a high-quality draft sequence of the genome.
Anomalies:
* the linker can appear (tandem,completely/partially) more than once
Links:
1_paired_end.pdf
Solexa/Illumina
Links:
Strep suis Solexa data set for download at Sanger ismb2007Poster.pdf Smith_Rennes_2007.pdf
Software:
* IO_LIB package /fs/sz-user-supported/common/packages/io_lib-1.11-x86_64/bin/ * STADEN package /fs/sz-user-supported/common/packages/staden-src-1-7-0/distrib/unix-rel-1-7-0/linux-bin
Assembly Formats
ace