Started MaSuRCA with mate pairs for Terebratalia 


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Using the following configuration file:

DATA
PE= pe 300 15  /sysdev/s9/bruno/assemblies/Terebratalia_transversa/data/Ttra_pe_trimmed1.fastq.gz  /sysdev/s9/bruno/assemblies/Terebratalia_transversa/data/Ttra_pe_trimmed2.fastq.gz
JUMP= sh 3000 450  /sysdev/s9/bruno/assemblies/Terebratalia_transversa/data/Ttra_mp3kb_trimmed1.fastq.gz  /sysdev/s9/bruno/assemblies/Terebratalia_transversa/data/Ttra_mp3kb_trimmed2.fastq.gz
JUMP= lg 5000 750  /sysdev/s9/bruno/assemblies/Terebratalia_transversa/data/Ttra_mp5kb_trimmed1.fastq.gz  /sysdev/s9/bruno/assemblies/Terebratalia_transversa/data/Ttra_mp5kb_trimmed2.fastq.gz
END

PARAMETERS
#this is k-mer size for deBruijn graph values between 25 and 101 are supported, auto will compute the optimal size based on the read data and GC content
GRAPH_KMER_SIZE=auto
#set this to 1 for Illumina-only assemblies and to 0 if you have 1x or more long (Sanger, 454) reads, you can also set this to 0 for large data sets with high jumping clone coverage, e.g. >50x
USE_LINKING_MATES=1
#this parameter is useful if you have too many jumping library mates. Typically set it to 60 for bacteria and something large (300) for mammals
LIMIT_JUMP_COVERAGE = 300
#these are the additional parameters to Celera Assembler.  do not worry about performance, number or processors or batch sizes -- these are computed automatically. for mammals do not set cgwErrorRate above 0.15!!!
CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.25 ovlMemory=4GB
#minimum count k-mers used in error correction 1 means all k-mers are used.  one can increase to 2 if coverage >100
KMER_COUNT_THRESHOLD = 1
#auto-detected number of cpus to use
NUM_THREADS= 32
#this is mandatory jellyfish hash size
JF_SIZE=5000000000
#this specifies if we do (1) or do not (0) want to trim long runs of homopolymers (e.g. GGGGGGGG) from 3' read ends, use it for high GC genomes
DO_HOMOPOLYMER_TRIM=0
END