Question: Best way to remove contaminants to get nuclear genome
gravatar for williamjohn360
6.7 years ago by
williamjohn36090 wrote:

I have plant genomic reads (WGS method) through hiseq 2000 with paired-end reads (read1.fastq, read2.fastq). I need to remove chloroplast and mitchondria reads to assemble only nuclear reads. I need to know which is best and fast way to remove contaminants

1. First doing genome assembly and remove mitochondria and chloroplast reads from genome using Blast.

2. Remove first mitochondria and chloroplast reads from fastq files by mapping reads to respective mitochondria and chloroplast read using bwa and get unmapped reads as nuclear reads as fastq file using samtools and picard and then do genome assembly.

assembly genome • 5.1k views
ADD COMMENTlink modified 6.7 years ago by Adrian Pelin2.4k • written 6.7 years ago by williamjohn36090

Question in topic: do you know how NCBI filters out mitochondrial contigs from submitted nuclear genome? I couldn't dig into that info.

ADD REPLYlink written 4.8 years ago by Pawel Osipowski20

where do you get the chloroplast and mitchondria genome sequence? NCBI? Thanks,

ADD REPLYlink written 3.3 years ago by fufuyou110
gravatar for JC
6.7 years ago by
JC12k wrote:

Option 2 is better, mapping with BWA is fast, and you are reducing the total reads to assembly, therefore your assembly time and complexity is reduced.

ADD COMMENTlink written 6.7 years ago by JC12k
gravatar for Adrian Pelin
6.7 years ago by
Adrian Pelin2.4k
Adrian Pelin2.4k wrote:

Option #2 works if there is a good reference available that is also very similar to what you have.

I would do a genome assembly, and then use MegaBlast against nt database to find our if each of your contigs is either mitochondrial/chloroplast or just a contaminants, and these guys I would put them in a list. I would then extract all contigs from that list, and use bwa to map reads against it, and extract unaligned reads to do your nuclear genome assembly.

ADD COMMENTlink written 6.7 years ago by Adrian Pelin2.4k
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