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Genomeweb published latest recommendation from 454 for Titanium De Novo Assembly of shotgun/paired end reads.
This information was given by Jim Knight, 454's director of bioinformatics development.
THe link is here:
Quote from 454's latest recommendation for De Novo Assembly with Newbler from above article:
"In order to perform de novo assemblies, the company currently recommends a combination of 8-kilobase shotgun and paired-end reads for bacterial genomes, he said. For larger genomes, it suggests customers use a combination of shotgun, 3-kilobase, 20-kilobase, and — as an option — 8-kilobase paired-end reads.
Knight recommended that users start assembling with a limited amount of sequence data and add more data to the mix as needed "to be able to stop when the assembly resolves and is no longer improving."
For bacterial artificial chromosomes, 454 recommends sequencing pools of 15 to 20 BACs with shotgun and 3-kilobase or 8-kilobase paired-end reads, according to Knight.
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3kb 8kb 20kb Titanium paired end kits are not out yet, but will be soon.
The above information should be relavent for De Novo projects using Titanium shotgun reads and paired end reads.
This information was given by Jim Knight, 454's director of bioinformatics development.
THe link is here:
Quote from 454's latest recommendation for De Novo Assembly with Newbler from above article:
"In order to perform de novo assemblies, the company currently recommends a combination of 8-kilobase shotgun and paired-end reads for bacterial genomes, he said. For larger genomes, it suggests customers use a combination of shotgun, 3-kilobase, 20-kilobase, and — as an option — 8-kilobase paired-end reads.
Knight recommended that users start assembling with a limited amount of sequence data and add more data to the mix as needed "to be able to stop when the assembly resolves and is no longer improving."
For bacterial artificial chromosomes, 454 recommends sequencing pools of 15 to 20 BACs with shotgun and 3-kilobase or 8-kilobase paired-end reads, according to Knight.
"
3kb 8kb 20kb Titanium paired end kits are not out yet, but will be soon.
The above information should be relavent for De Novo projects using Titanium shotgun reads and paired end reads.