Improving bacterial genome assembly

Sergioo

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Join Date: Oct 2013

Posts: 29
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#1

Improving bacterial genome assembly

10-19-2016, 08:49 AM

Deall seqanswers community, hope you are all doing well.
I have sequenced and assembled 8 bacterial genomes of the same species.
The initial assembly was constructed using paired-end reads from a Miseq and was rather satisfying (to draw first conclusion).
I also have long reads from PacBio of the same genomes and I would like to take advantage of both type of reads to improve my assembly and portray final conclusions with confidence. I am thinking of a scaffold approach whereby the Pacbio reads will be used to join contig. I would like you to guide me on a way forward.
I am not comfortable with Unix command line

Sincerely,
Tags: bacterial assembly, miseq reads, pacbio read
yzzhang

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Join Date: Jan 2013

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10-20-2016, 04:53 AM

Several tools such as SPAdes support hybrid assembly using illumina and pacbio reads. Their test suggested illumina reads only generated 92 contigs, while illumina+pacbio generated 5 contigs for E coli K12 using SPAdes.
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