Bioinformatics pipeline for Illumina MiSeq paired end data

[malandkib]

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!

[wdecoster]

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.

[malandkib]

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.

[GenoMax]

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?

[colindaven]

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.

https://github.com/fenderglass/ABruijn

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