View Triming Bb9001 and Velvet Assembly
time quality_trim -p Bb9001_1_trim.fasta -r -i Bb9001_1.fastq.fasta Bb9001_2.fastq.fasta -q -i Bb9001_1.fastq.fasta.qual Bb9001_2.fastq.fasta.qual
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Input reads: 63028492
Input residues: 6365877692
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Output reads: 41284176 65.50 %
Output residues: 3607586291 56.67 %
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Quality range: 2 to 41
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real 38m33.262s
user 15m0.960s
sys 1m9.510s
sequence_info Bb9001_1_trim.fasta
File Bb9001_1_trim.fasta Number of sequences 41284176 Residue counts: Total 3607586291 Sequence lengths: Minimum 51 Maximum 101 Average 87.38
Genome stimated size = 44Mb = 44000000 pb
exp_cov= (87*41284176)/44000000=81
time /opt/velvet_1.1.05/velveth auto_33 33 -fasta -shortPaired Bb9001_1_trim.fasta
real 29m3.811s
user 28m0.580s
sys 0m52.100s
time /opt/velvet_1.1.05/velvetg auto_33 -exp_cov 81 -ins_length 400 -cov_cutoff auto -shortMatePaired yes
real 84m39.112s
user 83m43.630s
sys 0m46.370s
sequence_info -n -r auto_33/contigs.fa
File auto_33/contigs.fa Number of sequences 36191 Residue counts: Number of A's 8288888 24.42 % Number of C's 7679095 22.62 % Number of G's 7682749 22.63 % Number of T's 8280794 24.39 % Number of N's 2017307 5.94 % Total 33948833 Sequence lengths: Minimum 65 Maximum 34574 Average 938.05 N50 3951
time clc_ref_assemble_long -o Bb9001_1_trim.fasta.cas -d auto_33/contigs.fa -q -p fb ss 100 400 -i Bb9001_1.fastq.fasta Bb9001_2.fastq.fasta
Progress: 100.0 %
real 28m6.971s
user 70m22.450s
sys 1m3.540s
assembly_info -p fb ss 100 400 Bb9001_1_trim.fasta.cas > Bb9001_1_trim.fasta.cas.txt
General info: Program name clc_ref_assemble_long Program version 4.01beta.59919 Program parameters -o Bb9001_1_trim.fasta.cas -d auto_33/contigs.fa -q -p fb ss 100 400 -i Bb9001_1.fastq.fasta Bb9001_2.fastq.fasta Contig files: auto_33/contigs.fa [ 36191 / 33948833 ] Read files: Bb9001_1.fastq.fasta interleaved with Bb9001_2.fastq.fasta [ 63028492 / 6365877692 ] <paired> Read info: Contigs 36191 Reads 63028492 Unmapped reads 5206399 8.26 % Mapped reads 57822093 91.74 % Multi hit reads 330500 0.57 % Paired 39081548 62.01 % Unpaired 23946944 37.99 % Paired end info: Paired reads 39081556 62.01 % Average distance 268.25 99.9 % of pairs between 100 - 399 99.0 % of pairs between 107 - 392 95.0 % of pairs between 127 - 371 Unpaired reads 23946936 37.99 % Both seqs not matching 2093932 8.74 % One seq not mathing 6224934 25.99 % Both seqs matching 15628070 65.26 % Different contigs 13262502 84.86 % Wrong directions 732006 4.68 % Too close 132 0.00 % Too far 1633430 10.45 % Coverage info: Mapped nucleotides 5488413105 86.22 % Total sites 33948833 Average coverage 161.67