khaper 去除基因组重复

该工具主要用于去除基因组重复的序列。

详情请查看githup

Note

• 软件需要内存 >100 G
• 该软件要求基因组大小 < 4G

简单使用

基本思路：将>40x的Illumina reads构建kmer 频率表，然后基于该频率表去除基因组重复的序列。

1.直接从githup下载即可，需要jellyfish，使用conda安装就可以

conda install -c bioconda jellyfish

2. 数据准备

• assemble.fasta
• reads1.gz
• reads2.gz

3. 构建kmer频率表

ls *.gz > fq.lst
 perl Bin/Graph.pl pipe -i fq.lst -m 2 -k 15 -s 1,3 -d Kmer_17

# 参数：
-m 最小kmer出现次数
-i fastq文件
-k kmer 大小
-d 输入文件
-s 如下所示
1: count k-mer by jellyfish
2: record unique k-mer into .h5 file
3: record unique k-mer into .bit file
4: record all k-mer into .h5 file
5: record all k-mer into .bit file
6: record all kmer into .bit with -m is 0.5 the peak
7: get the genome size, repeate rate and hete rate

注意：

# For k=17, we recommend:
perl Graph.pl pipe -i fq.lst -m 2 -k 17 -s 1,3,5 -d Kmer_17
# For k>17, we recommend:
 perl Graph.pl pipe -i fq.lst -m 2 -k 23 -s 1,2,4 -d Kmer_23

#######################################
k=15 is suitable for genome with size <100M.
k=17 is suitable for genome with size <10G.
This version is only support k<=17.

上述结果位于Kmer_17/02.Uinque_bit/kmer_17.bit

4. 去除基因组重复序列

perl remDup.pl <genome.fa> <outdir> <cutoff:0.7>

       Options:
              --ref   <str> The ref genome to build kbit
            --kbit  <str> The unique kmer file
              --kmer  <int> the kmer size [15]
            --sort  <int> sort seq by length [1]

如下命令

perl Bin/remDup.pl  --kbit Kmer_17/02.Uinque_bit/kmer_17.bit \
  --kmer 17 assemble.fasta Compress 0.3

结果位于：compress file: Compress/trinity.single.fasta.gz

注意：

a. If the compress file is larger than estimated genome size, turn down the  cutoff value
b. If the compress file is small than estimated genome size, turn up the  cutoff  value