Common scripts for sending and email Analysis (2) -- soapdenovo

1. soapdenovo configuration file example

Software Download Installation and Use: http://soap.genomics.org.cn/soapdenovo.html

ASM. cfg

#maximal read length
max_rd_len=100[LIB]avg_ins=450

#if sequence needs to be reversedreverse_seq=0

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

#use only first 100 bps of each readrd_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=3#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.gzq2=../../data/newBGIseq500_2.fq.gz

Run the script:

Run. Sh

/home/stu2/Software/Assemblathon1_pipeline/SOAPdenovo-63mer_v2.0 all -s  asm.cfg -K 35 -p 16 -R -o asm 1>cout.log 2>cerr.log

./SOAPdenovo-63mer_v2.0 pregraph -K 63 -s asm.cfg -o asm -p 40 1>pregraph.log 2>pregraph.err./SOAPdenovo-63mer_v2.0 contig -s asm.cfg -g asm -M 2 -e 1 -p 40 -R -D 2  1>contig.log 2>contig.err./SOAPdenovo-63mer_v2.0 map -s asm.cfg -g asm -k 31 -p 40 1>map.log 2>map.err./SOAPdenovo-63mer_v2.0 scaff -g asm -p 40  -F 1>scaff.log 2>scaff.err

02. Use of vcftools

Download and use the software:

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 7661779 --to-bp 7687550 --remove-indels --out TP53 --recode

03. Mutation Site Information Statistics

#!/usr/bin/perluse 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[9];     push @type, $line[10];     push @type, $line[11];     next;   }   my @line = split;   if ($line[1] >=7668402 && $line[1] <=7687550 && $line[2] ne "."){       my @type1 = split(/\/|:/, $line[9]);       my @type2 = split(/\/|:/, $line[10]);       my @type3 = split(/\/|:/, $line[11]);       #print "$type1[0]\t$type1[1]\n";       if ($type1[0]==$type1[1]){          $array[0][0] ++;       }else{          $array[0][1] ++;       }       if ($type2[0] == $type2[1]){           $array[1][0] ++;       }else{           $array[1][1] ++;       }       if($type3[0] == $type3[1]){           $array[2][0] ++;       }else{           $array[2][1] ++;        }   }}close IN;print "Sample\tHomozygous\tHeterozygote\n";print "$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";

Link: http://20xue.com/3997.html,https://www.cnblogs.com/azrael-cc/

Common scripts for sending and email Analysis (2) -- soapdenovo