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.
- install jellyfish
conda install -c bioconda jellyfish
- Prepare input files:
Prepare:
assemble.fasta # genemone assembly with dupplcated sequences.
PE300_1.fq.gz # read1
PE300_2.fq.gz # read2
- 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.
- 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