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View Bb9205 CLC Assembly

/data/process/Beauveria/Assemblies/Bb9205_Clean_CLC# time clc_novo_assemble -q -p fb ss 100 400 ../Bb9205_Clean_Velvet/Bb9205_1_trim.fasta -o Bb9205_trim.fasta
Progress: 96.6 %

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/remove_duplicates -p -r ../Bb9205_Clean_Velvet/Bb9205_1_trim.fasta -o Bb9205_trim_noDuplicates.fasta

time clc_novo_assemble -q -p fb ss 100 400 Bb9205_trim_noDuplicates.fasta -o Bb9205.fasta
Progress: 100.0 %
real 36m21.975s
user 74m58.500s
sys 0m10.300s

sequence_info -n -r Bb9205.fasta

File                           Bb9205.fasta

Number of sequences                  8065

Residue counts:
  Number of A's                   8690314   24.87 %
  Number of C's                   8715415   24.95 %
  Number of G's                   8721612   24.96 %
  Number of T's                   8679173   24.84 %
  Number of N's                    130614    0.37 %
  Total                          34937128

Sequence lengths:
  Minimum                             200
  Maximum                          102644
  Average                            4331.94
  N50                               12452

time /opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/clc_ref_assemble_long -o Bb9205.fasta.cas -d Bb9205.fasta -q -p fb ss 100 400 ../Bb9205_Clean_Velvet/Bb9205_1_trim.fasta
Progress: 100.0 %
real 17m1.098s
user 31m35.420s
sys 0m21.980s

assembly_info -p fb ss 100 400 Bb9205.fasta.cas > Bb9205.fasta.cas.txt

General info:

  Program name         clc_ref_assemble_long
  Program version      4.01beta.59919
  Program parameters   -o Bb9205.fasta.cas -d Bb9205.fasta -q -p fb ss 100 400 ../Bb9205_Clean_Velvet/Bb9205_1_trim.fasta

  Contig files:
    Bb9205.fasta [ 8065 / 34937128 ]

  Read files:
    ../Bb9205_Clean_Velvet/Bb9205_1_trim.fasta [ 38441560 / 3409205292 ] <paired>

Read info:

  Contigs                          8065
  Reads                        38441560
    Unmapped reads               496388    1.29 %
    Mapped reads               37945172   98.71 %
      Multi hit reads           1143365    3.01 %
    Paired                     33978032   88.39 %
    Unpaired                    4463528   11.61 %

Paired end info:

  Paired reads                 33978036   88.39 %
    Average distance                242.21
    99.9 % of pairs between         100 - 399
    99.0 % of pairs between         104 - 364
    95.0 % of pairs between         118 - 332

  Unpaired reads                4463524   11.61 %
    Both seqs not matching       300724    6.74 %
    One seq not mathing          391328    8.77 %
    Both seqs matching          3771472   84.50 %
      Different contigs         2529352   67.07 %
      Wrong directions          1002858   26.59 %
      Too close                  216510    5.74 %
      Too far                     22752    0.60 %

Coverage info:

  Mapped nucleotides         3316344029   97.28 %
  Total sites                  34937128
  Average coverage                   94.92