| Ensemble Assembler1.0 |
ensembleAssembly./config.txt |
PE = 260 30 read1.fq read2.fq |
|
./ensemble.sh |
NUM_THREADS = 8 |
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SOAP_KMER = 31 |
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ABYSS_KMER = 31 |
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METAVELVET_KMER = 31 |
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CON_LEN_DBG = 150 |
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CON_LEN_OLC = 300 |
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ASSEMBLY_MODE = VO, AaC, … |
| Cap3 (C) |
cap3 input.fasta |
| Minimo_amos-3.1.0 (O) |
Minimo input.fasta -D FASTA_EXP = 1 |
| SOAPdenovo2_r240 (S) |
SOAPdenovo-63mer all -K 31 -s read_soap.config -R -o read_soap |
max_rd_len = 600 |
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[LIB] |
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avg_ins = 260 |
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reverse_seq = 0 |
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asm_flags = 3 |
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rank = 1 |
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q1 = read1.fq |
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q2 = read2.fq |
| ABySS_1.3.7 (A) |
abyss-pe -C read_abyss name = read_abyss k = 31 in = ‘read1.fq read2.fq’ |
| MetaVelvet_1.2.10 (V) |
velveth read_velvet 31 -shortPaired -fastq read1.fq read2.fq && velvetg read_velvet -exp_cov auto -ins_length 260 && meta-velvetg read_velvet -ins_length 260 |
| Mira_4.0.2 (M) |
mira -t 8 read_mira.conf |
project = setAHumBac |
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parameters = -GE:not = 8 -DI:trt = /home/user/ -OUTPUT:rtd = yes |
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job = genome,denovo,accurate |
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readgroup = DataIlluminaPairedLib |
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autopairing |
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data = read1.fq read2.fq |
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technology = solexa |
| IDBA-UD_1.1.1(I) |
idba -r read.fa -o read_idba |
| Omega_v1.0.2 (G) |
omega -se 1 read.fq -l 60 -f read_omega |
| Celera_wgs-8.1 (W) |
fastqToCA -libraryname read_celera -technology none -mates read1.fq,read2.fq > read.frg |
|
runCA -d read_celera -p read_celera read.frg |
| MaSuRCA-2.2.0 (X) |
masurca config.txt && assemble.sh |
DATA |
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PE = pe 260 30 read1.fq read2.fq |
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END |
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|
PARAMETERS |
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GRAPH_KMER_SIZE = auto |
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USE_LINKING_MATES = 1 |
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LIMIT_JUMP_COVERAGE = 60 |
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CA_PARAMETERS = ovlMerSize = 30 cgwErrorRate = 0.25 ovlMemory = 4GB |
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KMER_COUNT_THRESHOLD = 1 |
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NUM_THREADS = 8 |
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JF_SIZE = 100000000 |
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DO_HOMOPOLYMER_TRIM = 0 |
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END |
| Trinity_r20140717 (T) |
Trinity –seqType fq –JM 25G –output read_trinity –left read1.fq –right read2.fq –CPU 8 |
