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Old 10-19-2011, 12:06 PM   #1
Seqasaurus
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Default illumina/454 de novo hybrid cDNA assembly with newbler2.6

Anybody experimented with hybrid assemblies using newbler 2.6?

I fed newbler 1.2 million titanium reads and 2.4 million 100-bp HiSeq2000 v3 reads (a random subset from 12 different treatments of total ~90 million reads). Everything was from cDNA and in fastq format. The result was fine compared to assembly of either set of reads alone. Took about 24 hours on an OK desktop.

About ~13000 contigs from 454, ~26,000 from illumina, 16,000 from hybrid.
Some 5' or 3' fragments in the 454 assembly were complete in the hybrid. Some contigs that were split in two in the illumina assembly were joined in the hybrid. Mapping all 90 million illumina reads onto the hybrid assembly with gsMapper also seemed fine. Took a couple of hours (quick output mode).

Will hopefully get around to doing a comparison with mira.
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Old 10-19-2011, 12:52 PM   #2
clostridium40
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I have done a couple of bacterial genomes (~5.5 Mb) as hybrid de novo assemblies using Newbler 2.6, I started with 112k paired end + 307k single end 454 reads at that resulted in 344 contigs with an N50 of 54,213. I then added 4 million 100 Illumina reads and that resulted in 295 contigs with an N50 of 71,796. I haven't done the Illumina reads alone, and I'm in the process of doing similar assemblies with MIRA. I would say on first couple of experiences the Newbler 2.6 seems to handle the Illumina reads okay, and it makes some difference. However, I can't say I'm overly impressed, there are several software programs out there designed to insert Illumina paired end reads in between assembled contigs that are more effective at closing gaps with additional Illumina sequencing.
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Old 01-23-2012, 08:20 AM   #3
LizBent
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Hi guys- what were the results of your tests using different hybrid assemblers? I am trying to figure out a pipeline for a 454/Illumina hybrid assembly and EST mapping (with the Illumina data) project.
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