Quality Trim

/data/process/Roya/Ensamblajes/illuminaAssembly$ time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/Hv387_1.fastq ../../RawDataRoya/Illumina/Originales/Hv387_2.fastq -p Hv387_trim.fasta

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/Hv494_1.fastq ../../RawDataRoya/Illumina/Originales/Hv494_2.fastq -p Hv494.fasta &

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/HvCat_1.fastq ../../RawDataRoya/Illumina/Originales/HvCat_2.fastq -p HvCat.fasta &

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/HvDQ952_1.fastq ../../RawDataRoya/Illumina/Originales/HvDQ952_2.fastq -p HvDQ952.fasta &

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/HvH_179_1.fastq ../../RawDataRoya/Illumina/Originales/HvH_179_2.fastq -p HvH_179.fasta &

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/ ../../RawDataRoya/Illumina/Originales/HvH_569_2.fastq -p HvH_569.fasta &

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/HvH_701_1.fastq ../../RawDataRoya/Illumina/Originales/HvH_701_2.fastq -p HvH_701.fasta &

time quality_trim -r -i ../../RawDataRoya/Illumina/Originales/HvMar_1.fastq ../../RawDataRoya/Illumina/Originales/HvMar_2.fastq -p HvMar.fasta &

Removing Duplicates

remove_duplicates -p -r Hv387_trim.fasta -o Hv387_trim_NoDupicates.fasta

remove_duplicates -p -r Hv494_trim.fasta -o Hv494_trim_NoDupicates.fasta &

remove_duplicates -p -r HvCat_trim.fasta -o HvCat_trim_NoDupicates.fasta &

Genome stimated size = 110Mb = 11000000 pb

Velvet Assembly

sequence_info sequence_info Hv387_trim_NoDupicates.fasta

File                           Hv387_trim_NoDupicates.fasta

Number of sequences              50782526

Residue counts:
  Total                        5405317372

Sequence lengths:
  Minimum                              55
  Maximum                             110
  Average                             106.44

exp_cov= (106*50782526)/110.000.000=49

time /opt/velvet_1.1.05/velveth HvH_179VelvetAsmK33 33 -fasta -shortPaired HvH_179_trim_NoDupicates.fasta
real 78m37.828s
user 74m26.870s
sys 1m15.360s

/opt/velvet_1.1.06/velvetg HvH_179VelvetAsmK33 -exp_cov 49 -ins_length 400 -cov_cutoff auto -shortMatePaired yes -amos_file yes

 /opt/scripts/fastasizefilter.pl HvH_179VelvetAsmK33/contigs.fa 200
sequence_info -n -r HvH_179VelvetAsmK33/contigs.fa.200

File                           HvH_179VelvetAsmK33/contigs.fa.200

Number of sequences                166629

Residue counts:
  Number of A's                  40142129   29.87 %
  Number of C's                  19473978   14.49 %
  Number of G's                  19450796   14.48 %
  Number of T's                  40096195   29.84 %
  Number of N's                  15204657   11.32 %
  Total                         134367755

Sequence lengths:
  Minimum                             200
  Maximum                           12986
  Average                             806.39
  N50                                1073

CLC Assembly

time clc_novo_assemble -q -p fb ss 100 400 Hv387_trim_NoDuplicatesTag.fasta -o Hv387CLCTag.fasta
Progress: 100.0 %
real 628m53.249s
user 956m36.390s
sys 1m14.670s

File	Hv387	Hv494	HvCat	HvDQ952	HvH_179	HvH_569	HvH_701	HvMar
Minimum	200	200	200	200	200	200	200	200
Maximum	45464	45679	31396	46233	59893	31087	46102	45663
Average	712.58	653.25	622.21	611.94	645.70	659.64	734.10	618.68
N50	1072	921	847	823	888	928	1131	832
Contigs	211495	211700	197394	197927	203770	202168	215628	203360