Bootstrap has its owned format of pagination, this gist is the configure to make pagination in Codeigniter matching with Bootstrap.

pagebation_bootstrap_setup.php

$this->load->library('pagination');

// Config Pagination
$config = array(
  'base_url'   	    => base_url(),
  'total_rows' 	    => 100,
  'per_page'        => 10,
  'full_tag_open'   => '<div class="pagination pagination-centered"><ul>',
  'full_tag_close'  => '</ul></div>',
  'first_link'      => $this->lang->line('First'),
  'first_tag_open'  => '<li>',
  'first_tag_close' =>'</li>',
  'last_link'       => $this->lang->line('Last'),
  'last_tag_open'   => '<li>',
  'last_tag_close'  => '</li>',
  'prev_link'       => $this->lang->line('Previous'),
  'prev_tag_open'   => '<li>',
  'prev_tag_close'  => '</li>',
  'next_link'       => $this->lang->line('Next'),
  'next_tag_open'   => '<li>',
  'next_tag_close'  => '</li>',
  'cur_tag_open'    => '<li class="active"><a>',
  'cur_tag_close'   => '</a></li>',
  'num_tag_open'    => '<li>',
  'num_tag_close'   => '</li>'
);
$this->pagination->initialize($config);

$data['pagination'] = $this->pagination->create_links();