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  • Bioinformatics pipeline for Illumina MiSeq paired end data

    Hello all!

    I am new to bioinformatics, so I am a little unclear as to the pipeline of analyzing data. My data is from a Nextera XT, dual indexing run. So far I have used a quality trimmer (trimmomatic) and placed the data into contigs and scaffolds (spades). Next, I plan on using Geneious to remove lengths of 500 bp or less and then I will annotate With Prokka.

    I am just curious as to what everyone else does to analyze data? Is what I'm doing the most accurate way?

    I am also analyzing data from the new instrument called the MinIon from Oxford Nanopore. Has anyone performed bioinformatics with data from this instrument yet? I was wondering what software you used and why.

    Thanks in advance!

  • #2
    You probably should say what organism you are working with and what your goal is with this experiment, since both hugely influence your toolbox of possibilities.

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    • #3
      You're right! I'm doing whole genome sequencing with 3 strains of E. coli. I am trying to determine what genes are present and comparing the genes present with the ones currently used to identify the organism.

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      • #4
        Sounds like SPAdes was not able to give you a single contig for each of the strains? Do you not have enough data? How many cycles of sequencing did you do?

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        • #5
          As far as the Minion goes, I was playing with the tool ABruijn yesterday. It worked very well for the bacterial example data and was easy to get going.



          Canu is probably the go to tool for Minion assembly so far, but can be technically tricky for large eukaryotic genomes.

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