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Thread | Thread Starter | Forum | Replies | Last Post |
Genome Res De novo bacterial genome sequencing: millions of very short reads assembly | b_seite | Literature Watch | 1 | 10-04-2017 11:26 PM |
The best genome de novo assembly software using hybrid data (Illumina, 454 & Sanger)? | Godevil | De novo discovery | 36 | 08-01-2012 02:25 AM |
PubMed: Rapid hybrid de novo assembly of a microbial genome using only short reads: C | Newsbot! | Literature Watch | 0 | 10-19-2011 11:40 PM |
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#1 |
Junior Member
Location: Austria Join Date: Mar 2017
Posts: 1
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Hi,
I would like to do an de novo genome assembly of a bacterial genome. I already have PacBio data and will now do Illumina sequencing, aditionally. I plan to do HiSeq, as I want to do a SNP analysis too. Which tool can a use to perform a hybrid assembly with PacBio and Illumina HiSeq data? PacBio gives me 5 contigs. Do you think that I can reduce the contigs with my HiSeq data? Thank you in advance!! |
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#2 |
Senior Member
Location: Cambridge Join Date: Sep 2010
Posts: 109
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A couple of points with respect of experimental design:
1. Make sure the Illumina libraries are PCR-free prep. 2. Unless you want to do 96 genomes on one hiseq lane, use MiSeq, since hiseq would give too much data (you would have to subsample), also to ensure that you do 2x250 or 2x300 read length. So use Miseq (~10-16 samples per 2x250 or 2x300 run) or Hiseq2500 in 2x250 rapid run mode. This would help the downstream analysis (pacbio error correction/assembly) quite a lot. (compared to 2x100 or 2x150 bps read length), especially in the repeat regions. Tools: Give spades assembler a try... |
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#3 |
Senior Member
Location: US Join Date: Dec 2010
Posts: 324
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Illumina data are very unlikely stitch your Pacbio contigs together. I would suggest to try different assemblers and parameters on your Pacbio data.
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