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I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations?

I'm currently using sickle for quality trimming. However, one of my samples have very low quality at the beginning as well and sickle doesn't seem to be able to deal well with it.

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    $\begingroup$ Hi there, looking at README of sickle "You can also change the length and quality thresholds for trimming, as well as disable 5'-trimming and enable truncation of sequences with Ns." which sort of suggests that it actually trims 5'. I feel like I am missing something. $\endgroup$
    – Kamil S Jaron
    Mar 12, 2019 at 15:02
  • $\begingroup$ Yes, I've tried that, but I've got the feeling it's too stringent for this particular sample. $\endgroup$
    – aLbAc
    Mar 12, 2019 at 15:50
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    $\begingroup$ Ah, now I get it. So you search for a tool that is configurable for quality trimming of 5' end, right? I would recommend edit your question and explain this. $\endgroup$
    – Kamil S Jaron
    Mar 12, 2019 at 16:16

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You can have a look at cutadapt. It is capable of quality trimming for both ends as you can read here.

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  • $\begingroup$ I've just tried this, however I still see the 5' quality still very low. I run it like this: cutadapt -q 30,30 -o output.fastq input.fastq Is there any thing else I'm missing? $\endgroup$
    – aLbAc
    Mar 12, 2019 at 15:49
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    $\begingroup$ Could you please give some quality summary information of your reads? Before and after the trimming? $\endgroup$
    – Mr_Z
    Mar 12, 2019 at 17:08
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I never spent too much time on choosing my trimming software, therefore I might have missed some jewels. I use trimmomatic when I need versatility and I am entirely sure that it trims reads on both ends. A more convenient option is skewer, they do perform quality filtering, but I could not find an explicit confirmation that it works on 5' too.

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Out of all of the major trimming tools available and widely used (trimmomatic, cutadapt/trimGalore (trimGalore is built on top of cutadapt), fastp), I actually instead prefer bbduk which is part of the bbmap suite:

https://github.com/BioInfoTools/BBMap

https://github.com/BioInfoTools/BBMap/blob/master/sh/bbduk.sh

It's much more "fine tuneable" than the other tools and runs in much less time using much less memory (as long as you set the memory limit as it's written mostly in java!). You can trim both ends or use a sliding window approach similar to what you see in Trimmomatic. Even better you can limit the number of bp in that it will trim from either left/right (5'/3'). It's by far the best all-around trimming tool for any type of sequencing dataset ({RNA, ChIP, PRO, GRO, ATAC, DNA}-seq etc...) in my opinion.

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