质控

  1. fastp --thread 4 \
  2.   -i ../data/SP1_1.fastq.gz \
  3.   -I ../data/SP1_2.fastq.gz \
  4.   -o SP1_1.fq.gz \
  5.   -O SP1_2.fq.gz \
  6.   -j SP1.fastp.json 
  7.   -h SP1.fastp.html \
  8.   2> SP1.fastp.log

组装

构建参考基因组index

  1. bowtie2-build   genome.fa  genome

将clean data比对到参考基因组

  1. bowtie2 -p 4 \
  2.   -x ./genome \
  3.   -1 SP1_1.fq.gz \
  4.   -2 SP1_2.fq.gz \
  5.   2> SP1.bowtie2.log | \
  6.   samtools view -h -f 4 | \
  7.   samtools fastq \
  8.     -1 un.SP1_1.fq.gz \
  9.     -2 un.SP1_2.fq.gz \
  10.     -s un.SP1_single.fq.gz

组装未必对reads

  • 使用megahit进行组装
  1. megahit \
  2.   -1 un.SP1_1.fq.gz,un.SP2_1.fq.gz \
  3.   -2 un.SP1_2.fq.gz,un.SP2_2.fq.gz \
  4.   -r un.SP1_single.fq.gz,un.SP2_single.fq.gz \
  5.   --min-contig-len 200 \
  6.   --tmp-dir  ./ \
  7.   --memory  0.4 \
  8.   --num-cpu-threads 10 \
  9.   --out-dir megahit \
  10.   --out-prefix  assembly
  13. seqtk seq -L 500 megahit/assembly.contigs.fa |  sed 's/^>/>novel./'  > megahit.fasta
  14. assembly-stats  megahit.fasta > megahit.fasta.stat
  • 使用soapdenovo进行组装
  1. mkdir soapdenovo
  3. SOAPdenovo-63mer all \
  4.   -s ./soapdenovo_config.txt \
  5.   -o  soapdenovo/assembly \
  6.   -K 41 -p 10 -d 1 -F -M 3 -R \
  7.   1> soapdenovo.log \
  8.   2> soapdenovo.err
  10. GapCloser -l 151 -t 10 \
  11.   -a soapdenovo/assembly.scafSeq \
  12.   -b soapdenovo_config.txt \
  13.   -o soapdenovo/assembly.scafSeq.gapclo.fa
  15. seqtk seq -L 500 soapdenovo/assembly.scafSeq.gapclo.fa | sed 's/^>/>novel./' > soapdenovo.fasta