Hi,
In order to get an assembly, I use Trimmomatic for bad quality and adapters trimming.
My question is, should I do an error correction for my data ?
1) If yes, before or after Trimmomatic.
2) I know only ErrorCorrectReads.pl from ALLPATHS-lg (http://software.broadinstitute.org/allpaths-lg/blog/?p=559). Can you recommend an other good one ?
edit: my data are illumina PE and MP.
2 answers
Usually error correction is to be done after adaptor trimming. If you perform error correction you need not trim ends for low quality bases as the error correction doesn't change base-quality values but changes the read-bases only.
Error correction is definitely recommended for denovo assembly when you work with illumina data. Since you have PE-reads, you would be going for de-bruijin assemblers which would create kmer overlaps based on the read data. If there are kmer errors you either create a misassembly or no assembly based on the assembly parameters specifying the kmer coverage.
I have used Musket before, which worked like a charm on my data at-least.
https://sourceforge.net/projects/musket/
bbnorm also performs error correction -
For a main-stream assembler nowadays, if it needs error correction, it will come with an error corrector it prefers. For example, spades comes with hammer. SGA/allpaths-lg use their own correctors. Long-read assemblers pack falcon_sense etc by default. I would recommend to just use the error corrector the assembler recommends. Sometimes, the overall best error corrector does not necessarily deliver the best assembly because tools all make trade off here and there; the right combination is often more important.
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why you tend to do error correction?!
You know, correct errors so you don't have errors in your assembly. It's not that weird.
Yes, I knew your mean. However, I didn't see this correction as a general part of an analysis in the published papers (maybe I'm wrong). So, I wanted to know is there any specific reason for it?
there is some workflow that implement this idea also some tools like jabba "tool to correct PacBio read using short read" implement other tools that first correct the short reads it self
What type of data are you using?
Illumina PE and nextera MP
yes you should do after trimming
Tools: EC: an efficient error correction algorithm for short reads
QuorUM: An Error Corrector for Illumina Reads.