Hi,
I am doing de novo assembly with a lot of 454 and Illumina data that i have for my 7.3 Mb bacterial genome.
Data i have:
1.5 million 454 FLX and Titanium reads (average length ~320 bp)
160 000 mate-pair mates from a 10 kb 454 Tit library
33 million Illumina reads (36 bp)
Given a lack of computing power, i've been using the Celera Assembler to assemble, de novo, the 454 data, and it has been giving nice results, with scaffolds up to 3.3 Mb and contigs up to 480 kb.
Independently, I've used EDENA to assemble the Illumina data (i can't use velvet - not enough RAM), getting contigs up to 17 Kb.
Ideally, I'd use MIRA to do a combined 454/Illumina assembly, but i can't given my lack of RAM.
What I'd like to do is take the EDENA/Illumina contigs and incorporate them into the Celera Assembly. This was done similarly with vcake/Illumina contigs into Newbler/454 in this paper:
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
However, I don't know how to incorporate the EDENA/Illumina contigs so that they can be used by Celera assembler. Has anyone done this?
Any guidance would be appreciated!
I am doing de novo assembly with a lot of 454 and Illumina data that i have for my 7.3 Mb bacterial genome.
Data i have:
1.5 million 454 FLX and Titanium reads (average length ~320 bp)
160 000 mate-pair mates from a 10 kb 454 Tit library
33 million Illumina reads (36 bp)
Given a lack of computing power, i've been using the Celera Assembler to assemble, de novo, the 454 data, and it has been giving nice results, with scaffolds up to 3.3 Mb and contigs up to 480 kb.
Independently, I've used EDENA to assemble the Illumina data (i can't use velvet - not enough RAM), getting contigs up to 17 Kb.
Ideally, I'd use MIRA to do a combined 454/Illumina assembly, but i can't given my lack of RAM.
What I'd like to do is take the EDENA/Illumina contigs and incorporate them into the Celera Assembly. This was done similarly with vcake/Illumina contigs into Newbler/454 in this paper:
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
However, I don't know how to incorporate the EDENA/Illumina contigs so that they can be used by Celera assembler. Has anyone done this?
Any guidance would be appreciated!
