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.
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.