High throughput paired-end sequencing of large-insert clone libraries

A method comprising:

• (a) incorporating genomic nucleic acid insert ranging between approximately 10-1000 kb into a cloning site of an F-plasmid-derived vector, wherein said cloning site comprises at least two polylinkers and is flanked by at least one adapter sequence pair and a nicking endonuclease site pair, thereby creating a fosmid;
• (b) transfecting said fosmid into a microbe capable of being transfected by said F-plasmid-derived vector, thereby forming a fosmid clone library;
• (c) amplifying said fosmid library in vivo by growing said library of transfected microbes in a suitable culture medium,
• (d) extracting and purifying said circular fosmids;
• (e) cleaving said cloned inserts to create a first portion and a second portion, wherein said first portion is less than said second portion, and said first portion remains attached to said F-plasmid-derived cloning vector, and said second portion is released from said cloning vector;
• (f) recircularizing said cloning vector by co-ligating the terminal ends of said first portion;
• and
• (g) amplifying said first portion by inverse polymerase chain reaction using said universal primer pair, thereby creating a plurality of linear amplicons configured for at least one next-generation sequencing platform.

A method comprising:

• (a) sequencing short read genomic inserts from a ShaRc fosmid fragment library, wherein said library comprises said short read genomic inserts and a fosmid plasmid derived cloning vector sequence, with a next-generation sequencing platform;
• and
• (b) assembling said short read genomic inserts into a complete genome using a microprocessor comprising a genome assembly algorithm,
• wherein said genome assembly algorithm comprises a step for trimming said fosmid plasmid derived cloning vector sequence from said short read genomic inserts.