给参考基因组建立index

faidx index

samtools faidx *.fa

Usage: samtools faidx <file.fa|file.fa.gz> [<reg> [...]]
Option: 
 -o, --output FILE        Write FASTA to file.
 -n, --length INT         Length of FASTA sequence line. [60]
 -c, --continue           Continue after trying to retrieve missing region.
 -r, --region-file FILE   File of regions.  Format is chr:from-to. One per line.
 -i, --reverse-complement Reverse complement sequences.
     --mark-strand TYPE   Add strand indicator to sequence name
                          TYPE = rc   for /rc on negative strand (default)
                                 no   for no strand indicator
                                 sign for (+) / (-)
                                 custom,<pos>,<neg> for custom indicator
     --fai-idx      FILE  name of the index file (default file.fa.fai).
     --gzi-idx      FILE  name of compressed file index (default file.fa.gz.gzi).
 -f, --fastq              File and index in FASTQ format.
 -h, --help               This message.

bwa index

bwa index -a bwtsw *.fa -p *.fa

Usage:   bwa index [options] <in.fasta>

Options: -a STR    BWT construction algorithm: bwtsw, is or rb2 [auto]
         -p STR    prefix of the index [same as fasta name]
         -b INT    block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.* 

Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
         `-a div' do not work not for long genomes.

picard index

java -jar picard.jar CreateSequenceDictionary \
R = *.fa \
O = *.dict

picard index 参数较多，暂不列出