测序：
RNA-seq：100X
nanopore：80X
resequence：30X
质控：
使用fastp对RNAseq和Resequence测序数据进行质控
Resequence Q20，Q30 皆为100%
RNAseq Q20，90% Q30，89%
基因组Survey
FG12
jellyfish.sh
pre=Kmer_19
ls ../resequence/FG12C/1.Cleandata/FG12C.IS300-400bp_Clean.*.fq.gz | awk '{print "gzip -dc "$0 }' > generate.file
/ifs1/Software/bin/jellyfish count -t 4 -C -m 19 -s 1G -g generate.file -G 2 -o $pre
/ifs1/Software/bin/jellyfish histo -v -o $pre.histo $pre -t 4 -h 10000
/ifs1/Software/bin/jellyfish stats $pre -o $pre.stat
image.png
image.png
/ifs1/Grp8/haozhigang/training20200405/genomics_training/41.Assembly/01.kmer_analysis/gce-1.0.2/gce -f Kmer_19.histo -c 26 -g 1140936461 -M 10000 >gce.table 2>gce.log
gce.log
Rscript ~/training20200405/genomics_training/41.Assembly/01.kmer_analysis/genomescope-master/genomescope.R Kmer_19.histo 19 150 ./ 100000
summary.txt
FG7
pre=Kmer_19
ls ../resequence/FG7C/1.Cleandata/FG7C.IS300-400bp_Clean.*.fq.gz | awk '{print "gzip -dc "$0 }' > generate.file
/ifs1/Software/bin/jellyfish count -t 4 -C -m 19 -s 1G -g generate.file -G 2 -o $pre
/ifs1/Software/bin/jellyfish histo -v -o $pre.histo $pre -t 4 -h 10000
/ifs1/Software/bin/jellyfish stats $pre -o $pre.stat
image.png
image.png
/ifs1/Grp8/haozhigang/training20200405/genomics_training/41.Assembly/01.kmer_analysis/gce-1.0.2/gce -f Kmer_19.histo -c 26 -g 1141618012 -M 10000 >gce.table 2>gce.log
gce.log
Rscript ~/training20200405/genomics_training/41.Assembly/01.kmer_analysis/genomescope-master/genomescope.R Kmer_19.histo 19 150 ./ 100000
summary.txt
image.png
基因组拼接
使用wtdbg2
## 组装
/ifs1/Software/bin/wtdbg2 \
-t 6 -x ont -g 37M -L 500 -l 500 -e 2 \
-i /ifs1/Grp8/haozhigang/nanopore_data/FG11C/1.Cleandata/FG11C.filtered_reads.fq.gz \
-o FG11_ont
## 得到一致性序列
### wtdbg-cns 2分钟
/ifs1/Software/biosoft/wtdbg2/wtdbg-cns \
-t 6 \
-i FG11_ont.ctg.lay.gz \
-f \
-o FG11_ont.wtdbg-cns.fa
### wtpoa-cns 稍慢 12 分钟
/ifs1/Software/biosoft/wtdbg2/wtpoa-cns\
-t 6 \
-i FG11_ont.ctg.lay.gz \
-f \
-o FG11_ont.wtpoa-cns.fa
基因组pilon
draft_genome=/ifs1/Grp8/haozhigang/training20200405/genomics_training/41.Assembly/06.assembly_wtdbg2/FG12_ont.wtpoa-cns.fa
fq1=/ifs1/Grp8/haozhigang/RNAseq/Filter_SOAPnuke/Clean/FG12B/FG12B_clean_1.fq.gz
fq2=/ifs1/Grp8/haozhigang/RNAseq/Filter_SOAPnuke/Clean/FG12B/FG12B_clean_2.fq.gz
ln -s $draft_genome ./genome_FG12.fa
bwa index genome_FG12.fa
bwa mem -t 6 genome_FG12.fa $fq1 $fq2 | /ifs1/Software/bin/samtools sort - -o reads_FG12.bam
samtools index reads_FG12.bam
java -Xmx80G -jar /ifs1/Software/biosoft/pilon/pilon-1.23.jar \
--genome $draft_genome \
--frags reads_FG12.bam \
--changes --vcf --diploid --threads 6 \
--outdir ./pilon_out_FG12 --output genome_pilon_FG12
image.png
gc-depth
minimap2 -ax map-ont genome_pilon_FG12.fasta FG12C.filtered_reads.fq.gz| /pub/software/samtools/samtools sort - -o aln_sort.bam
genome=genome_pilon_FG12.fasta
bam=aln_sort.bam
prefix=gcdep
window=500
step=250
# 计算序列长度
seqtk comp $genome | awk '{print $1"\t"$2}' > $prefix.len
# 划分窗口 生成bed文件
bedtools makewindows -w $window -s $step -g $prefix.len > $prefix.window.bed
# 按窗口提取序列并计算gc含量
seqtk subseq $genome $prefix.window.bed > $prefix.window.fasta
seqtk comp $prefix.window.fasta |awk '{print $1 "\t" ($4+$5)/($3+$4+$5+$6) } ' > $prefix.window.gc
# 按窗口计算平均深度
bedtools coverage -b aln_sort.bam -a gcdep.window.bed -mean | awk '{print $1":"$2+1"-"$3"\t"$4}' > $prefix.window.depth
# 绘图
Rscript run_gcdep.R $prefix.window.gc $prefix.window.depth $prefix.pdf 0 0.8 0 500
gc-depth
由图可知，存在一部分低GC含量的片段，推测可能是污染所以，一方面比对NT库，另一方面截取低GC区的片段，重新进行比对。
NT库比对命令及结果
blastn -db nt -query genome_pilon_FG12.fasta -outfmt 10 -num_alignments 5 -max_hsps 1 -out blast-output.m6
NT库比对结果
低GC区片段
#寻找小于30%片段
seqtk comp gcdep.window.fasta |awk '{print $1 "\t" ($4+$5)/($3+$4+$5+$6) } ' |awk '$2<0.3'|less -S
seqtk subseq ../genome_pilon_FG12.fasta sample.txt>1.txt
nucmer -c 200 -g 200 -p out 1.txt PH-1.fa
show-coords -c -d -l -I 95 -L 10000 -r out.delta > out.show
mummerplot -f -l -p out -s large -t png out.delta
/pub/software/gnuplot4.6.7/bin/gnuplot out.gp
低GC片段比对PH-1
由图可知，低GC区域片段全部比对到PH-1上面，不是污染
MUMER作图
nucmer -c 200 -g 200 -p out genome_pilon_FG12.fasta PH-1.fa
show-coords -c -d -l -I 95 -L 10000 -r out.delta > out.show
mummerplot -f -l -p out -s large -t png out.delta
/pub/software/gnuplot4.6.7/bin/gnuplot out.gp
mummer
由图可知，ctg2和ctg5为一条序列，所以加一个中间序列100N，cat命令。最后得到4条序列和一条染色体。
image.png
Repeat注释
# 构建数据库
/pub/software/RepeatModeler-2.0.1/BuildDatabase -name sesame test_data/genome.fasta
# 运行 RepeatModeler
/pub/software/RepeatModeler-2.0.1/RepeatModeler -database sesame -pa 20 -LTRStruct
# 运行 RepeatMasker
/pub/software/RepeatMasker/RepeatMasker -pa 20 -qq -lib sesame-families.fa test_data/genome.fasta >repeatmasker.log 2>&1
# 生成RepeatLandscape
/pub/software/RepeatMasker/util/calcDivergenceFromAlign.pl -s sesame.divsum test_data/genome.fasta.cat
perl /pub/software/RepeatMasker/util/createRepeatLandscape.pl -div sesame.divsum -g 18577337 > sesame.html
