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dsarov / MGAP

An automated assembly pipeline for microbial genomes
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trimmomatic #4

Closed mictadlo closed 8 years ago

mictadlo commented 8 years ago

Hi, In order to change the trimmomatic settings do I have to do it here?

Trimmomatic could improve the assembly bu using the MAXINFO settings rather than SLIDINGWINDOW as they described in their paper.

Did you try to use MAXINFO setting or to use for example QuorUM an error corrector for Illumina reads?

Thank you in advance.

Mic

dsarov commented 8 years ago

Hi Mic,

Yes, that is the correct location for trimmomatic settings. I haven't tested QuorUM or MAXINFO. I used to use fastx toolkit but found the handling of read pairing a bit clunky. With the way the pipeline is written it should be straightforward to chop and change the programs it uses as long as you know a bit of bash scripting. Just check the input and output files and make sure the file tests are correct.

I found that anything more than a very light trim affects read scaffolding negatively. Often even fairly low quality bases are useful information. Light filtering seems to improve assemblies over a larger variety of input data but this step is probably highly dependent on what information you are feeding the pipeline.

Good luck!

Derek