Samtools

samtools is a tool operating sam and bam files for collection. It contains a number of commands.

faidx: fasta indexed file, the resulting index files to .fai suffix ending.

Genomic index file 
$ samtools faidx genome.fasta 

generated index file genome.fasta.fai, is a text file, divided into five. 
The first column is the name of the sub-sequence; 
the second column is the length of the sequence; 

the last number is the size of the file genome.fasta; 4 and 5 do not know what is meant. 

This file can be located in the storage position sequence fasta file on disk, directly and quickly recall sequences. 

Because the index file, the following command can be used quickly extracted from the genome sequences to fasta format 
$ samtools faidx genome.fasta scffold_10> scaffold_10.fasta

Reference Source:

http://www.chenlianfu.com/?p=1399