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View Bb9119 Velvet Assembly

Assembly Clean data Bb9119 with Velvet

Quality Trim

time quality_trim -p Bb9119_1_trim.fasta -r -i Bb9119_1.fastq.fasta Bb9119_2.fastq.fasta -q -i Bb9119_1.fastq.fasta.qual Bb9119_2.fastq.fasta.qual

Input reads: 51550802
Input residues: 5206631002

Output reads: 39766865 77.14 %
Output residues: 3378690943 64.89 %

Quality range: 2 to 41

real 19m38.636s
user 12m16.320s
sys 0m51.220s

Results of Quality Trim

sequence_info Bb9119_1_trim.fasta

File                           Bb9119_1_trim.fasta

Number of sequences              33188332

Residue counts:
  Total                        2865501772

Sequence lengths:
  Minimum                              51
  Maximum                             101
  Average                              86.34

Genome stimated size = 44Mb = 44000000 pb
exp_cov= (87*33188332)/44000000=65

Assembly Bb9119

time /opt/velvet_1.1.05/velveth auto_33 33 -fasta -shortPaired Bb9119_1_trim.fasta
real 25m8.468s
user 22m58.860s
sys 0m30.460s

time /opt/velvet_1.1.05/velvetg auto_33 -exp_cov 65 -ins_length 400 -cov_cutoff auto -shortMatePaired yes -amos_file yes
real 76m25.955s
user 70m51.840s
sys 0m36.690s

sequence_info -n -r Bb9119_Clean_Velvet.fasta.200

 File                           Bb9119_Clean_Velvet.fasta.200

Number of sequences                  9414

Residue counts:
  Number of A's                   6945403   24.19 %
  Number of C's                   6924060   24.11 %
  Number of G's                   6914930   24.08 %
  Number of T's                   6956836   24.23 %
  Number of N's                    973270    3.39 %
  Total                          28714499

Sequence lengths:
  Minimum                             200
  Maximum                           42900
  Average                            3050.19
  N50                                6143

clc_ref_assemble_long -o Bb9119_trim.fasta.cas -d Bb9119_Clean_Velvet.fasta.200 -q -p fb ss 100 400 ../../TrimDataBeauveria/Bb9119_trim_tag.fasta

assembly_info -p fb ss 100 400 Bb9119_trim.fasta.cas > Bb9119_trim.fasta.cas.txt

General info:

  Program name         clc_ref_assemble_long
  Program version      4.01beta.59919
  Program parameters   -o Bb9119_trim.fasta.cas -d Bb9119_Clean_Velvet.fasta.200 -q -p fb ss 100 400 ../../TrimDataBeauveria/Bb9119_trim_tag.fasta

  Contig files:
    Bb9119_Clean_Velvet.fasta.200 [ 9414 / 28714499 ]

  Read files:
    ../../TrimDataBeauveria/Bb9119_trim_tag.fasta [ 33188332 / 2865501772 ] <paired>

Read info:

  Contigs                          9414
  Reads                        33188332
    Unmapped reads              3274420    9.87 %
    Mapped reads               29913912   90.13 %
      Multi hit reads             62642    0.21 %
    Paired                     24703052   74.43 %
    Unpaired                    8485280   25.57 %

Paired end info:

  Paired reads                 24703054   74.43 %
    Average distance                278.09
    99.9 % of pairs between         106 - 400
    99.0 % of pairs between         128 - 394
    95.0 % of pairs between         156 - 370

  Unpaired reads                8485278   25.57 %
    Both seqs not matching      1787064   21.06 %
    One seq not mathing         2974712   35.06 %
    Both seqs matching          3723502   43.88 %
      Different contigs         3014074   80.95 %
      Wrong directions           125390    3.37 %
      Too close                   20096    0.54 %
      Too far                    563942   15.15 %

Coverage info:

  Mapped nucleotides         2517635008   87.86 %
  Total sites                  28714499
  Average coverage                   87.68

Assembly with other Parameters

/opt/velvet_1.1.06/velvetg Bb9119VelvetK33 -exp_cov 65 -ins_length 400 -cov_cutoff auto -shortMatePaired yes -amos_file yes -unused_reads yes