Library

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A library is a collection of inserts that were all created together, by a particular sequencing method, in a particular laboratory. Each insert in a library contains one or more reads; if it contains multiple ones, the reads are paired-production reads. Important library statistics include number of inserts and average insert size (mean and standard deviation).

The inserts in a library are all of a particular type, and the insert size depends on that type. Plasmid inserts are typically around 4 kbp in length, although there exists a "long plasmid" type that averags 10 kbp. Fosmid inserts average 40kbp, while BAC end inserts are around 100kbp. (These sizes are hard-wired into ComputeLibraryClusters in the form of the default value of INSERT_SIZES.) It is important to realize that these are typical numbers, not guarantees: a library's average insert size may vary widely, and the standard deviation may be high. A typical full-coverage assembly project includes around 4x plasmid coverage, 2x fosmid coverage, and 1x BAC coverage, for a total of 7x.

In Arachne

In Arachne input, library information is found in the XML ancillary files. Each read is tagged with a library_id or seq_lib_id indicating the name of the library it comes from. Output files that provide library data include assembly.ps.

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