<p>You can have a look at <a href="https://cutadapt.readthedocs.io/en/stable/installation.html" rel="nofollow noreferrer">cutadapt</a>. It is capable of quality trimming for both ends as you can read <a href="https://cutadapt.readthedocs.io/en/stable/guide.html#quality-trimming" rel="nofollow noreferrer">here</a>.</p>

CC BY-SA 4.0
2019-03-12T15:49:11.737Z
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?
aLbAc
CC BY-SA 4.0
2019-03-12T17:08:46.540Z
Could you please give some quality summary information of your reads? Before and after the trimming?
Mr_Z
CC BY-SA 4.0
2019-03-12T15:33:32.753Z
2019-03-12T15:33:32.753Z
Mr_Z
<p>I never spent too much time on choosing my trimming software, therefore I might have missed some jewels. I use <a href="http://www.usadellab.org/cms/?page=trimmomatic" rel="nofollow noreferrer">trimmomatic</a> when I need versatility and I am entirely sure that it trims reads on both ends. A more convenient option is <a href="https://github.com/relipmoc/skewer" rel="nofollow noreferrer">skewer</a>, they do perform quality filtering, but I could not find an explicit confirmation that it works on 5' too.</p>

CC BY-SA 4.0
2019-03-12T15:12:58.773Z
2019-03-12T15:12:58.773Z
Kamil S Jaron
<p>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:</p>

<p><a href="https://github.com/BioInfoTools/BBMap" rel="nofollow noreferrer">https://github.com/BioInfoTools/BBMap</a></p>

<p><a href="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbduk.sh" rel="nofollow noreferrer">https://github.com/BioInfoTools/BBMap/blob/master/sh/bbduk.sh</a></p>

<p>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.</p>

CC BY-SA 4.0
2019-03-22T20:29:29.557Z
2019-03-22T20:29:29.557Z
Margaret Gruca
<p>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? </p>

<p>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. </p>

CC BY-SA 4.0
2019-03-12T15:02:19.210Z
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.
Kamil S Jaron
CC BY-SA 4.0
2019-03-12T15:50:29.823Z
Yes, I've tried that, but I've got the feeling it's too stringent for this particular sample.
aLbAc
CC BY-SA 4.0
2019-03-12T16:16:19.447Z
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.
Kamil S Jaron
<ngs><illumina><quality-control><trimming>
Tools for quality trimming at 5 prime?
# Tools for quality trimming at 5 prime?

(Asked by: username_0 on 2019-03-12)

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.

**Tags:** ngs, illumina, quality-control, trimming
> **Comments:**
> **username_1**: 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.  
> **username_0**: Yes, I've tried that, but I've got the feeling it's too stringent for this particular sample.  
> **username_1**: 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.  

---

## 3 answers

### Answer by username_2 on 2019-03-12. Score: 4

You can have a look at [cutadapt](https://cutadapt.readthedocs.io/en/stable/installation.html). It is capable of quality trimming for both ends as you can read [here](https://cutadapt.readthedocs.io/en/stable/guide.html#quality-trimming).

> **Comments:**
> **username_0**: 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?  
> **username_2**: Could you please give some quality summary information of your reads? Before and after the trimming?  

---

### Answer by username_1 on 2019-03-12. Score: 3

I never spent too much time on choosing my trimming software, therefore I might have missed some jewels. I use [trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) when I need versatility and I am entirely sure that it trims reads on both ends. A more convenient option is [skewer](https://github.com/relipmoc/skewer), they do perform quality filtering, but I could not find an explicit confirmation that it works on 5' too.


---

### Answer by username_3 on 2019-03-22. Score: 2

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.


---

