View Bb9205 Velvet Assembly
Assembly Clean data Bb9205 with Velvet
Quality Trim
time quality_trim -p Bb9205_1_trim.fasta -r -i Bb9205_1.fastq.fasta Bb9205_2.fastq.fasta -q -i Bb9205_1.fastq.fasta.qual Bb9205_2.fastq.fasta.qual
Input reads: 54987574
Input residues: 5553744974
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Output reads: 38441560 69.91 %
Output residues: 3409205292 61.39 %
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Quality range: 2 to 41
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real 31m52.077s
user 13m0.630s
sys 0m59.100s
Results of Quality Trim
sequence_info Bb9205_1_trim.fasta
File Bb9205_1_trim.fasta Number of sequences 38441560 Residue counts: Total 3409205292 Sequence lengths: Minimum 51 Maximum 101 Average 88.69
Genome stimated size = 44Mb = 44000000 pb
exp_cov= (88*38441560)/44000000=76
Assembly Bb9205
time /opt/velvet_1.1.05/velveth auto_33 33 -fasta -shortPaired Bb9205_1_trim.fasta
real 116m54.080s
user 104m4.900s
sys 1m12.190s
time /opt/velvet_1.1.05/velvetg auto_33 -exp_cov 76 -ins_length 400 -cov_cutoff auto -shortMatePaired yes
real 99m55.565s
user 91m27.890s
sys 0m51.990s
sequence_info -n -r auto_33/contigs.fa
File auto_33/contigs.fa Number of sequences 20248 Residue counts: Number of A's 7499762 24.35 % Number of C's 7287857 23.66 % Number of G's 7290606 23.67 % Number of T's 7495295 24.33 % Number of N's 1228491 3.99 % Total 30802011 Sequence lengths: Minimum 65 Maximum 45292 Average 1521.24 N50 5436
time clc_ref_assemble_long -o Bb9205_1_trim.fasta.cas -d auto_33/contigs.fa -q -p fb ss 100 400 -i Bb9205_1.fastq.fasta Bb9205_2.fastq.fasta
real 43m17.507s
user 62m0.390s
sys 1m6.340s
assembly_info -p fb ss 100 400 Bb9205_1_trim.fasta.cas > Bb9205_1_trim.fasta.cas.txt
General info: Program name clc_ref_assemble_long Program version 4.01beta.59919 Program parameters -o Bb9205_1_trim.fasta.cas -d auto_33/contigs.fa -q -p fb ss 100 400 -i Bb9205_1.fastq.fasta Bb9205_2.fastq.fasta Contig files: auto_33/contigs.fa [ 20248 / 30802011 ] Read files: Bb9205_1.fastq.fasta interleaved with Bb9205_2.fastq.fasta [ 54987574 / 5553744974 ] <paired> Read info: Contigs 20248 Reads 54987574 Unmapped reads 5821036 10.59 % Mapped reads 49166538 89.41 % Multi hit reads 245493 0.50 % Paired 34676216 63.06 % Unpaired 20311358 36.94 % Paired end info: Paired reads 34676224 63.06 % Average distance 238.03 99.9 % of pairs between 100 - 399 99.0 % of pairs between 103 - 368 95.0 % of pairs between 115 - 333 Unpaired reads 20311350 36.94 % Both seqs not matching 2674228 13.17 % One seq not mathing 6293616 30.99 % Both seqs matching 11343506 55.85 % Different contigs 9382024 82.71 % Wrong directions 1474842 13.00 % Too close 194 0.00 % Too far 486446 4.29 % Coverage info: Mapped nucleotides 4574911009 82.38 % Total sites 30802011 Average coverage 148.53