This is a software for remove dupplication for genome.

Note:

• This software Need > 100G memory

• This version on GitHub is only support reference <4000M

• Please contact us: tanger.zhang@gmail.com

Usage:

We firstly use >40x Illumina reads to build the kmer frequency table. Then use this kmer table to compress the reference.

1. install jellyfish

conda install -c bioconda jellyfish

2. Prepare input files:

Prepare:

assemble.fasta 	# genemone assembly with dupplcated sequences.
PE300_1.fq.gz		# read1
PE300_2.fq.gz		# read2

3. Build the kmer frequency table:

ls *.gz > fq.lst
perl Bin/Graph.pl pipe -i fq.lst -m 2 -k 15 -s 1,3 -d Kmer_15

#result:
kmer bit file: Kmer_15/02.Uinque_bit/kmer_15.bit

Note:

​ a. k=15 is suitable for genome with size <100M.

​ b. k=17 is suitable for genome with size <10G.

​ c. This version is only support k<=17.

4. Compress the assembly file

# compress the genome

# Usage:
 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]

Description
     This script is to remove dupplcation seq

# Demo
perl Bin/remDup.pl  --kbit Kmer_15/02.Uinque_bit/kmer_15.bit --kmer 15 assemble.fasta Compress 0.3

# result:
compress file: Compress/trinity.single.fasta.gz

Note:

​ 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