基因组拼接探索

生信喵

1 不同 kmer 大小

1. mkdir 1.kmer
   
2. cd 1.kmer
   
3. cp ../36.illumina/lib.list .
   
4. SOAPdenovo-31mer all -s lib.list -K 31 -o kmer31 -D 1 -d 1 -u 2 -p 12 >kmer31.log
   
5. SOAPdenovo-63mer all -s lib.list -K 63 -o kmer63 -D 1 -d 1 -u 2 -p 12 >kmer63.log
   
6. SOAPdenovo-127mer all -s lib.list -K 127 -o kmer105 -D 1 -d 1 -u 2 -p 12 >kmer105.log
   
7. 
   
8. ll *.scafSeq
   
9. seqkit stat *.scafSeq
   
10. mv *.scafSeq ../
    
11. rm -rf kmer*
    
12. #修改-d
    
13. SOAPdenovo-63mer all -s lib.list -K 63 -o kmer63 -D 1 -d 0 -u 2 -p 12 >kmer63_0.log
    
14. SOAPdenovo-63mer all -s lib.list -K 63 -o kmer63 -D 1 -d 1 -u 2 -p 12 >kmer63_1.log
    
15. SOAPdenovo-63mer all -s lib.list -K 63 -o kmer63 -D 1 -d 2 -u 2 -p 12 >kmer63_2.log
    
16. seqkit stat *.scafSeq

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2 文库大小
小片段文库，写入文件 lib.list

1. #大片段文库
   
2. max_rd_len=150
   
3. [LIB]
   
4. avg_ins=500
   
5. reverse_seq=0
   
6. asm_flags=3
   
7. rank=1
   
8. pair_num_cutoff=3
   
9. q1=/cleandata/500_clean.1.fq.gz
   
10. q2=/cleandata/500_clean.2.fq.gz
    
11. 
    
12. [LIB]
    
13. avg_ins=2000
    
14. reverse_seq=1
    
15. asm_flags=2
    
16. rank=2
    
17. pair_num_cutoff=3
    
18. q1=/cleandata/2000_clean.1.fq.gz
    
19. q2=/cleandata/2000_clean.2.fq.gz
    
20. 
    
21. SOAPdenovo-63mer all -s lib.list -K 63 -o kmer1 -D 1 -d 1 -u 2 -p 12 >kmer1.log
    
22. SOAPdenovo-63mer all -s lib2.list -K 63 -o kmer2 -D 1 -d 1 -u 2 -p 12 >kmer2.log
    
23. 
    
24. ll *.scafSeq
    
25. seqkit stat *.scafSeq
    
26. seqkit seq -m 500 kmer1.scafSeq | seqkit stat
    
27. seqkit seq -m 500 kmer2.scafSeq | seqkit stat

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换spades软件看大片段文库

1. echo "spades.py --isolate -o spades1 -t 12 -1 /share/home/xiehs/05.assembly/data/illumina._1.fastq.gz -2 /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz -t 12 1>spades1.log 2>spades1.err" > spades.sh
   
2. echo "spades.py --isolate -o spades2 -t 12 -1 /share/home/xiehs/05.assembly/data/illumina._1.fastq.gz -2 /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz -t 12 --mp1-1 /cleandata/2000_clean.1.fq.gz --mp1-2 /cleandata/2000_clean.2.fq.gz 1>spades2.log 2>spades2.err" >> spades.sh
   
3. nohup sh spades.sh &
   
4. seqkit seq -m 500 spades1/scaffolds.fasta | seqkit stat
   
5. seqkit seq -m 500 spades2/scaffolds.fasta | seqkit stat

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3 数据质量
比较过滤前后拼接结果差别；

1. mkdir 3.filter
   
2. SOAPdenovo-63mer all -s lib.list -K 63 -o kmer63 -D 1 -d 0 -u 2 -p 12 >kmer63.log
   
3. seqkit seq -m 500 kmer63.scafSeq | seqkit stat
   
4. seqkit seq -m 500 ../1.kmer/kmer63_1.scafSeq | seqkit stat

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4 数据量大小
分别抽取 10%，30%，50%，80%进行比较。

1. seqkit sample -p 0.1 -s 1234 /share/home/xiehs/05.assembly/data/illumina_1.fastq.gz | gzip >reads.0.1_1.fq.gz
   
2. seqkit sample -p 0.1 -s 1234 /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz | gzip >reads.0.1_2.fq.gz
   
3. 
   
4. for i in {0.1,0.3,0.5,0.8};do
   
5.     seqkit sample -p ${i} -s 1234 /share/home/xiehs/05.assembly/data/illumina_1.fastq.gz | gzip >reads.${i}_1.fq.gz
   
6.     seqkit sample -p ${i} -s 1234 /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz | gzip >reads.${i}_2.fq.gz;
   
7. done;
   
8. ls -1 *.fq.gz | xargs -n 2 | while read {i,j};do echo spades.py -o spades_${i} -t 12 -1 ${i} -2 ${j};done;
   
9. spades.py -o spades_reads.0.1_1.fq.gz -t 12 -1 reads.0.1_1.fq.gz -2 reads.0.1_2.fq.gz
   
10. spades.py -o spades_reads.0.3_1.fq.gz -t 12 -1 reads.0.3_1.fq.gz -2 reads.0.3_2.fq.gz
    
11. spades.py -o spades_reads.0.5_1.fq.gz -t 12 -1 reads.0.5_1.fq.gz -2 reads.0.5_2.fq.gz
    
12. spades.py -o spades_reads.0.8_1.fq.gz -t 12 -1 reads.0.8_1.fq.gz -2 reads.0.8_2.fq.gz
    
13. 
    
14. _1.fq.gz删掉作为目录-o
    
15. 
    
16. nohup sh spades.sh &
    
17. seqkit stat spades_reads*/scaffolds.fasta

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5 reads 长度的影响

1. #不同reads长度
   
2. #利用wgsim分别模拟长度70与150bp长度reads
   
3. cp /share/home/xiehs/05.assembly/data/MGH78578.fasta .
   
4. wgsim MGH78578.fasta read.50_1.fq read.50_2.fq -1 50 -2 50
   
5. wgsim MGH78578.fasta read.300_1.fq read.300_2.fq -1 300 -2 300
   
6. 
   
7. spades.py -o spades50 -t 12 -1 read.50_1.fq -2 read.50_2.fq
   
8. spades.py -o spades300 -t 12 -1 read.300_1.fq -2 read.300_2.fq
   
9. seqkit stat spades50/scaffolds.fasta
   
10. seqkit stat spades300/scaffolds.fasta

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6 不同错误率

1. #不同错误率的影响
   
2. wgsim -e 0.01 -1 50 -2 50 MGH78578.fasta read.0.01_1.fq read.0.01_2.fq
   
3. wgsim -e 0.1 -1 50 -2 50 MGH78578.fasta read.0.1_1.fq read.0.1_2.fq
   
4. #用soapdenovo拼接
   
5. SOAPdenovo-63mer all -s lib.list -K 35 -o kmer35 -D 1 -d 1 -u 2 -p 12
   
6. SOAPdenovo-63mer all -s lib.list -K 35 -o kmer35_01 -D 1 -d 1 -u 2 -p 12
   
7. seqkit stat kmer35.scafSeq

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