Question

Close Bacterial Draft Genome With Other Draft Genome

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10.7 years ago

biotech ▴ 570

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

genomics assembly • 4.1k views

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.7 years ago by biotech ▴ 570

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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 REPLY • link 10.7 years ago by Xingyu Yang ▴ 280

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

ADD REPLY • link 10.7 years ago by biotech ▴ 570

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Sorry for late reply. Here's the pipeline I usually use.

Alignment with bowtie2
samtools mpileup -uf <Fasta of Reference> <Alignment Results>.bam | bcftools view -cg - | vcfutils.pl vcf2fq > <Assembled Results>.cons.fq

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 10.7 years ago by Xingyu Yang ▴ 280

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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 REPLY • link 10.6 years ago by Torst ▴ 980

Ram · Answer 1 · 2014-09-23

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10.2 years ago

mesabioinformatics ▴ 30

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

https://github.com/fenderglass/Ragout

Hope it helps!

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by mesabioinformatics ▴ 30

Ram · Answer 2 · 2014-09-16

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 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.