For #1: geecee from EMBOSS.

For #2:

how can i split multi fasta file into separate fasta files by contigs name? (original fasta have ~32000 contig and after separation i must have 32000 fasta file)

Jim Kent's (UCSC) faSplit utility is the fastest solution. You will need to do chmod a+x faSplit to add execute permissions after you download the file.

faSplit - Split an fa file into several files.
usage:
   faSplit how input.fa count outRoot
where how is either 'about' 'byname' 'base' 'gap' 'sequence' or 'size'.

1.how can i receive GC-content profile for a given window-size (50000) for a reference genome in fasta file?

I would do a cut -c xx-yy where xx and yy are the two margins (included) of the region you're interested. Once you have that, you can easily count the number of G+C and divide it by the total number of chars.

2.how can i split multi fasta file into separate fasta files by contigs name? (original fasta have ~32000 contig and after separation i must have 32000 fasta file)

I personally would make a python script. Something like:

#!/usr/bin/env python

import sys 

for line in sys.stdin:
  if line[0:1] == ">":
    if OUT:
      OUT.close()
    name = # process your line accordingly to get the sequence / scaffold name
    OUT = open("{0}.fa".format(name), "w")
    OUT.write(line)
  else:
    OUT.write(line)
else:
  OUT.close()

Then you:

• chmod 755 pythonscript.py
• cat filename.fa | pythonscript.py

Be careful: making that many files will clog your machine.