Question: Close Bacterial Draft Genome With Other Draft Genome
0
gravatar for biotech
3.7 years ago by
biotech500
United States
biotech500 wrote:

Hi,

I would like to reduce contig number of the bacterial draft genome I'm trying to close. The draft genome is in 47 contigs and has been assembled by me, using Phred, Phrap, Consed.

I'm thinking in using the other draft genome that has been published (same bacterial specie) perform this task.

Do you think I should start from zero, that is, join the not assembled raw data of the two drafts published and see what happens, or use a tool having as input the two assembled drafts?

Thanks for you help, Bernardo

assembly genomics • 1.8k views
ADD COMMENTlink modified 3.2 years ago by mesabioinformatics30 • written 3.7 years ago by biotech500

If you already have a good reference, why not directly use reference based assembly? If you want to identify variations, it might not be a good idea to assembly them together or merge them. It can also be difficult to say which sample your data comes from.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Xingyu Yang260

Do you know any good tool to do reference based assembly?

ADD REPLYlink written 3.7 years ago by biotech500

Sorry for late reply. Here's the pipeline I usually use. 1. Alignment with bowtie2 2. samtools mpileup -uf <fasta of="" reference=""> <alignment results="">.bam | bcftools view -cg - | vcfutils.pl vcf2fq > <assembled results="">.cons.fq

ADD REPLYlink written 3.7 years ago by Xingyu Yang260

It is unlikely that the other draft genome has any information you can use for your draft genome. I would reckon the assembly will be broken at the same places ie. large repeats such as rRNA locii and insertion sequences that your read length can not span.

ADD REPLYlink written 3.6 years ago by Torst860
3
gravatar for mesabioinformatics
3.2 years ago by
United States
mesabioinformatics30 wrote:

Try: Ragout—a reference-assisted assembly tool for bacterial genomes

http://bioinformatics.oxfordjournals.org/content/30/12/i302.abstract 

https://github.com/fenderglass/Ragout

 

Hope it helps !

ADD COMMENTlink modified 3.2 years ago by Istvan Albert ♦♦ 75k • written 3.2 years ago by mesabioinformatics30
0
gravatar for Chrispin Chaguza
3.2 years ago by
University of Liverpool, UK
Chrispin Chaguza220 wrote:

If you have contigs of your draft genome, you can order and orient them according to the published reference sequence (genome) of the same or closely related species. In order to do this, you can use abacas (http://abacas.sourceforge.net/Manual.html) to contiguate your genome and it can also automatically design primers for you so that you can sequence the 'gapped' regions and close the genome. Another bacterial genome finishing tool that you could use is CONTIGuator (http://contiguator.sourceforge.net/).

ADD COMMENTlink written 3.2 years ago by Chrispin Chaguza220
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