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View Bb9024 CLC Assembly

Assembly Clean data Bb9024 with CLC

time /opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/clc_novo_assemble -q -p fb ss 100 400 ../Bb9024_Clean_Velvet/Bb9024_1_trim.fasta -o Bb9024_trim.fasta
real 42m23.096s
user 103m4.280s
sys 0m15.630s

time clc_ref_assemble_long -o Bb9024_trim.fasta.cas -d Bb9024_trim.fasta -q -p fb ss 100 400 -q ../Bb9024_Clean_Velvet/Bb9024_1_trim.fasta
Progress: 100.0 %
real 20m52.233s
user 48m59.500s
sys 0m52.140s

sequence_info -n -r Bb9024_trim.fasta

File                           Bb9024_trim.fasta

Number of sequences                 22714

Residue counts:
  Number of A's                  10425210   25.31 %
  Number of C's                   9977674   24.22 %
  Number of G's                   9980336   24.23 %
  Number of T's                  10402045   25.25 %
  Number of N's                    404529    0.98 %
  Total                          41189794

Sequence lengths:
  Minimum                             200
  Maximum                           91881
  Average                            1813.41
  N50                                8307

assembly_info -p fb ss 100 400 Bb9024_trim.fasta.cas > Bb9024_trim.fasta.cas.txt

General info:

  Program name         clc_ref_assemble_long
  Program version      4.01beta.59919
  Program parameters   -o Bb9024_trim.fasta.cas -d Bb9024_trim.fasta -q -p fb ss 100 400 -q ../Bb9024_Clean_Velvet/Bb9024_1_trim.fasta

  Contig files:
    Bb9024_trim.fasta [ 22714 / 41189794 ]

  Read files:
    ../Bb9024_Clean_Velvet/Bb9024_1_trim.fasta [ 30385592 / 2661147963 ] <paired>

Read info:

  Contigs                         22714
  Reads                        30385592
    Unmapped reads               639682    2.11 %
    Mapped reads               29745910   97.89 %
      Multi hit reads            268495    0.90 %
    Paired                     26001414   85.57 %
    Unpaired                    4384178   14.43 %

Paired end info:

  Paired reads                 26001426   85.57 %
    Average distance                258.49
    99.9 % of pairs between         102 - 391
    99.0 % of pairs between         115 - 368
    95.0 % of pairs between         148 - 350

  Unpaired reads                4384166   14.43 %
    Both seqs not matching       154224    3.52 %
    One seq not mathing          970916   22.15 %
    Both seqs matching          3259026   74.34 %
      Different contigs         2992416   91.82 %
      Wrong directions           207822    6.38 %
      Too close                   35044    1.08 %
      Too far                     23744    0.73 %

Coverage info:

  Mapped nucleotides         2558660742   96.15 %
  Total sites                  41189794
  Average coverage                   62.12