生信分析常用脚本（二）--SOAPdenovo

1.SOAPDenovo配置文件示例

软件下载安装和使用：http://soap.genomics.org.cn/soapdenovo.html

asm.cfg

#maximal read length
max_rd_len=

[LIB]
avg_ins=450

#if sequence needs to be reversed
reverse_seq=0

#in which part(s) the reads are used
asm_flags=3

#use only first 100 bps of each read
rd_len_cutoff=100

#in which order the reads are used while scaffolding
rank=1

# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=../../data/newBGIseq500_1.fq.gz
q2=../../data/newBGIseq500_2.fq.gz

运行脚本：

run.sh

/home/stu2/Software/Assemblathon1_pipeline/SOAPdenovo-63mer_v2. all -s  asm.cfg -K  -p  -R -o asm >cout.log >cerr.log

./SOAPdenovo-63mer_v2. pregraph -K  -s asm.cfg -o asm -p  >pregraph.log >pregraph.err
./SOAPdenovo-63mer_v2. contig -s asm.cfg -g asm -M  -e  -p  -R -D   >contig.log >contig.err
./SOAPdenovo-63mer_v2. map -s asm.cfg -g asm -k  -p  >map.log >map.err
./SOAPdenovo-63mer_v2. scaff -g asm -p   -F >scaff.log >scaff.err

02. VCFtools的使用

软件下载和使用：

https://vcftools.github.io/documentation.html

https://vcftools.github.io/man_latest.html

# get Qual
./vcftools --gzvcf chr17.vcf.gz --site-quality --out Qual
# get interval
./vcftools --gzvcf chr17.vcf.gz --chr chr17 --from-bp  --to-bp  --remove-indels --out TP53 --recode

03.变异位点信息统计

#!/usr/bin/perl
use strict;

my $file = shift;

open(In,"gzip -dc $file|") or die ("can't open the file!\n");

my @type;
my @array = ( );
while(<In>){
   chomp;
   next if (/^##/);
   if (/^#/){
     my @line = split;
     push @type, $line[];
     push @type, $line[];
     push @type, $line[];
     next;
   }
   my @line = split;
   if ($line[] >= && $line[] <= && $line[] ne "."){
       my @type1 = split(/\/|:/, $line[]);
       my @type2 = split(/\/|:/, $line[]);
       my @type3 = split(/\/|:/, $line[]);
       #print "$type1[0]\t$type1[1]\n";
       if ($type1[]==$type1[]){
          $array[][] ++;
       }else{
          $array[][] ++;
       }
       if ($type2[] == $type2[]){
           $array[][] ++;
       }else{
           $array[][] ++;
       }
       if($type3[] == $type3[]){
           $array[][] ++;
       }else{
           $array[][] ++;
        }
   }
}
close IN;

print "Sample\tHomozygous\tHeterozygote\n";
print "$type[0]: $array[0][0]\t$array[0][1]\n";
print "$type[1]: $array[1][0]\t$array[1][1]\n";
print "$type[2]: $array[2][0]\t$array[2][1]\n";

04. KmerFreq使用脚本

工具包地址：ftp://public.genomics.org.cn/BGI/SOAPdenovo2

kmer.sh

./kmerfreq -k  -l lib.list -t  >17mer.freq >17mer.log

lib.list

 reads1.fq.gz
 reads2.fq.gz

友情参考链接：http://20xue.com/3997.html，https://www.cnblogs.com/azrael-cc/