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View Bb9001 CLC Assembly

Assembly Clean data Bb9001 with CLC

time clc_novo_assemble -q -p fb ss 100 400 ../Bb9001_Clean_Velvet/Bb9001_1_trim.fasta -o Bb9001_trim.fasta
Progress: 100.0 %
real 90m5.447s
user 118m41.340s
sys 0m19.510s

sequence_info -n -r Bb9001_trim.fasta

File                           Bb9001_trim.fasta

Number of sequences                 10436

Residue counts:
  Number of A's                   9197298   24.94 %
  Number of C's                   9111891   24.71 %
  Number of G's                   9124624   24.74 %
  Number of T's                   9190875   24.92 %
  Number of N's                    256247    0.69 %
  Total                          36880935

Sequence lengths:
  Minimum                             200
  Maximum                           74727
  Average                            3534.01
  N50                               11067

time clc_ref_assemble_long -o Bb9001_trim.fasta.cas -d Bb9001_trim.fasta -q -p fb ss 100 400 -q ../Bb9001_Clean_Velvet/Bb9001_1_trim.fasta
Progress: 100.0 %
real 24m15.745s
user 36m58.070s
sys 0m31.750s

assembly_info -p fb ss 100 400 Bb9001_trim.fasta.cas > Bb9001_trim.fasta.cas.txt

General info:

  Program name         clc_ref_assemble_long
  Program version      4.01beta.59919
  Program parameters   -o Bb9001_trim.fasta.cas -d Bb9001_trim.fasta -q -p fb ss 100 400 -q ../Bb9001_Clean_Velvet/Bb9001_1_trim.fasta

  Contig files:
    Bb9001_trim.fasta [ 10436 / 36880935 ]

  Read files:
    ../Bb9001_Clean_Velvet/Bb9001_1_trim.fasta [ 41284176 / 3607586291 ] <paired>

Read info:

  Contigs                         10436
  Reads                        41284176
    Unmapped reads               732811    1.78 %
    Mapped reads               40551365   98.22 %
      Multi hit reads            442484    1.09 %
    Paired                     33855140   82.01 %
    Unpaired                    7429036   17.99 %

Paired end info:

  Paired reads                 33855152   82.01 %
    Average distance                269.41
    99.9 % of pairs between         101 - 399
    99.0 % of pairs between         108 - 389
    95.0 % of pairs between         130 - 368

  Unpaired reads                7429024   17.99 %
    Both seqs not matching       147330    1.98 %
    One seq not mathing         1170962   15.76 %
    Both seqs matching          6110732   82.25 %
      Different contigs         5418398   88.67 %
      Wrong directions           414780    6.79 %
      Too close                  106468    1.74 %
      Too far                    171086    2.80 %

Coverage info:

  Mapped nucleotides         3473845218   96.29 %
  Total sites                  36880935
  Average coverage                   94.19