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MCB3895-004 Lecture # 12 Oct 2/14

MCB3895-004 Lecture # 12 Oct 2/14. The many meanings of assembly quality; De novo genome assembly options. Discussion. What types of "good" assemblies are there?. Assembly options. Different sequencing technologies & libraries

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MCB3895-004 Lecture # 12 Oct 2/14

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  1. MCB3895-004 Lecture #12Oct 2/14 The many meanings of assembly quality; De novo genome assembly options

  2. Discussion • What types of "good" assemblies are there?

  3. Assembly options • Different sequencing technologies & libraries • Trimmomatic: adapter removal, trimming low quality bases or reads • Read error correction: SGA: $ sga • De novo assemblers: • ABySS2: $ ABYSS • Celera Assembler $ runCA • MaSuRCA: $ masurca • MIRA $ mira • SPAdes $ spades.py • SOAPdenovo $ SOAPdenovo-127mer • Velvet $ velveth/velvetg • Software parameters, e.g., kmer size

  4. A useful script • http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl • Requires Falite.pm be in the same directory: http://korflab.ucdavis.edu/Unix_and_Perl/FAlite.pm • May need to change this: Old: foreach my $base qw (A C G T N){ New: my @bases_array; foreach my $base (@bases_array){ Also present later: foreach my $size qw ( … ){

  5. A simpler bash script for qsub #!/bin/bash #$ -S /bin/bash # change to a preexisting working directory # .sh script does not need to be in this directory cd $HOME/temp # execute the job from the current working directory #$ -cwd # assumes that "something.pl" is in the # directory "~/temp/" perl something.pl > out

  6. Today - assignment #4 continued • Design ON PAPER a strategy that you think will create an effective de novo assembly • Discuss this strategy with me BEFORE touching the computer • Execute your strategy • Based on your results, revise your strategy and try again

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