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Old 09-27-2011, 07:34 AM   #1
ZhigangLi
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Location: Beijing, China

Join Date: Nov 2010
Posts: 11
Default Problem with hybrid assebly with Celera Assembly

Hello, everyone,

Celera Assembler(CA) 6.1 can do hybrid assembly now.

I have 3 types of reads, Solexa (100bp read length, 500bp insert length), Sanger and 454. The species is a fungi(~40M). I want to assemble them using CA.

At the beginning, I combined 454 and Sanger data and assembled them using CA. I'm somewhat satisfied with its performance. There are ~38M in scaffolds.

However, I combined all three types of data and then did assembly as well. The result was so bad that only 1M in contigs and scaffolds. why?

Here is my spec file:
# -------------------------------------

utgErrorRate=0.03
utgErrorLimit=2.5 # Allow mismatches over and above the utgErrorRate. This helps with Illumina reads.

merSize = 22
overlapper=ovl
#
unitigger = bog
utgBubblePopping = 1


# MERYL calculates K-mer seeds
merylMemory = 64000
merylThreads = 20

# OVERLAPPER calculates overlaps
ovlMemory = 4GB
ovlThreads = 20

# OVERLAP STORE build the database
ovlStoreMemory = 8192 # Mbp

# ERROR CORRECTION applied to overlaps
frgCorrThreads = 10
frgCorrConcurrency = 3

ovlCorrBatchSize = 1000000
ovlCorrConcurrency = 10

# CONSENSUS configuration
cnsConcurrency = 10

#output
createACE=1
merQC=1
merQCmemory=10240
cleanup=light

# -------------------------------------


Could someone help me with this problem?
I would appreciate any help.
Thanks.
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