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
—
Output reads: 38441560 69.91 %
Output residues: 3409205292 61.39 %
—
Quality range: 2 to 41
—
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