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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

Input reads: 63028492
Input residues: 6365877692

Output reads: 41284176 65.50 %
Output residues: 3607586291 56.67 %

Quality range: 2 to 41

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