Navigation

 ·   Wiki Home
 ·   Data Processing
 ·   Hemileia vastatrix
 ·   Hypothenemus hampei
 ·   Coffea
 ·   Beauveria bassiana
 ·  
 ·   Title List
 ·   Uncategorized Pages
 ·   Random Page
 ·   Recent Changes
 ·   Wiki Help
 ·   What Links Here

Active Members:

Search:

 

Create or Find Page:

 

View Bb9024 Velvet Assembly

Assembly Clean data Bb9024 with Velvet

Quality Trim

quality_trim -p Bb9024_1_trim.fasta -r -i Bb9024_1.fastq.fasta Bb9024_2.fastq.fasta -q -i Bb9024_1.fastq.fasta.qual Bb9024_2.fastq.fasta.qual
Input reads: 44996554
Input residues: 4544651954

Output reads: 30385592 67.53 %
Output residues: 2661147963 58.56 %

Quality range: 2 to 41

Results of Quality Trim

sequence_info Bb9024_1_trim.fasta

 File                           Bb9024_1_trim.fasta

Number of sequences              30385592

Residue counts:
  Total                        2661147963

Sequence lengths:
  Minimum                              51
  Maximum                             101
  Average                              87.58

Genome stimated size = 44Mb = 44000000 pb
exp_cov= (87*30385592)/44000000=60

Assembly Bb9024

time /opt/velvet_1.1.05/velveth auto_33 33 -fasta -shortPaired Bb9024_1_trim.fasta
real 128m6.560s
user 112m40.300s
sys 1m43.140s

time /opt/velvet_1.1.05/velvetg auto_33 -exp_cov 60 -ins_length 400 -cov_cutoff auto -shortMatePaired yes
real 62m34.078s
user 61m32.800s
sys 0m32.230s

sequence_info -n -r auto_33/contigs.fa

File                           auto_33/contigs.fa

File                           auto_33/contigs.fa

Number of sequences                 34786

Residue counts:
  Number of A's                   8396233   24.36 %
  Number of C's                   7974388   23.13 %
  Number of G's                   7986209   23.17 %
  Number of T's                   8385982   24.33 %
  Number of N's                   1728271    5.01 %
  Total                          34471083

Sequence lengths:
  Minimum                              65
  Maximum                           36383
  Average                             990.95
  N50                                5046

time clc_ref_assemble_long -o Bb9024_1_trim.fasta.cas -d auto_33/contigs.fa -q -p fb ss 100 400 -i Bb9024_1.fastq.fasta Bb9024_2.fastq.fasta

assembly_info -p fb ss 100 400 Bb9024_1_trim.fasta.cas > Bb9024_1_trim.fasta.cas.txt

less Bb9024_1_trim.fasta.cas.txt

General info:

  Program name         clc_ref_assemble_long
  Program version      4.01beta.59919
  Program parameters   -o Bb9024_1_trim.fasta.cas -d auto_33/contigs.fa -q -p fb ss 100 400 -i Bb9024_1.fastq.fasta Bb9024_2.fastq.fasta

  Contig files:
    auto_33/contigs.fa [ 34786 / 34471083 ]

  Read files:
    Bb9024_1.fastq.fasta interleaved with Bb9024_2.fastq.fasta [ 44996554 / 4544651954 ] <paired>

Read info:

  Contigs                         34786
  Reads                        44996554
    Unmapped reads              3324009    7.39 %
    Mapped reads               41672545   92.61 %
      Multi hit reads            232373    0.56 %
    Paired                     29948492   66.56 %
    Unpaired                   15048062   33.44 %

Paired end info:

  Paired reads                 29948494   66.56 %
    Average distance                258.10
    99.9 % of pairs between         102 - 398
    99.0 % of pairs between         113 - 377
    95.0 % of pairs between         139 - 347

  Unpaired reads               15048060   33.44 %
    Both seqs not matching      1422722    9.45 %
    One seq not mathing         3802574   25.27 %
    Both seqs matching          9822764   65.28 %
      Different contigs         8654838   88.11 %
      Wrong directions           343584    3.50 %
      Too close                      54    0.00 %
      Too far                    824288    8.39 %

Coverage info:

  Mapped nucleotides         3956332310   87.05 %
  Total sites                  34471083
  Average coverage                  114.77