Best trimming tool

Question

[int11ap1]

What tool do you use for removing adapters and low-quality portions of reads and why?

Answer 1

[Ian]

Our facility uses Trimmomatic as it performs adapter trimming and various other read filtering/trimming functions. It is pair-aware maintaining paired filtered reads whilst removing singletons. It is simple to use and reasonably fast.

Answer 2

[GenoMax]

This thread won't be complete without bbduk and seal(which is part of BBMap suite). Written in pure java will work on PC/Mac/*nix.

Answer 3

[Juke34]

Best ? I don't know but there is lot of tools fairly comprehensive and efficient.

See this answer

It could be interesting to have a comparaison of the different tools in order to assess their main differences.

Table 5.1 here could be a good start.

Answer 4

[dariober]

Personally I'm happy with cutadapt although I haven't explored other options, apart from trim_galore which is a wrapper around cutadapt. Things I like of cutadapt:

• Fast enough, easy to use, flexible in how/what you want to trim and what to get back
• Great documentation, well maintained.
• Write to stdout so you can stream through bwa (or else) without writing massive files to disk
• Recent releases: Read and write interleaved paired-end reads which can also be streamed to bwa

About quality trimming, these days quality is very high up to 150+ bases so I usually skip it altogether.

I superficially compared cutadapt with the trimmer that comes with the pipeline in Illumina/Basespace and the results where very similar, I think Basespace's trimmer was a little more aggressive, but essentially same results.

Answer 5

[Gabriel R.]

Our group at the Max Planck wrote a paper comparing the accuracy of various trimming algorithm. Our Bayesian trimmer leeHom (http://grenaud.github.io/leeHom/) outperformed other algorithms in terms of accuracy and very favorably in terms of speed:

It achieves merger of overlapping portions and detection of chimeric reads. You do not need cutoffs for % of matches etc and it eats fastq and BAM.

For the low quality, I would not recommend cutting reads at they will be harder to map but you remove low quality reads, I coded something a while back.

It uses BAM files and can filter on the exp. number of mismatches and sequence entropy.

Hope this helps!

Answer 6

[Antonio R. Franco]

You also need to take into account the possibility of run the trimmer in parallel (using several cores) and considering how fast it works actually

For example. In a 20Gb genomic fastq sequence (only one of the paired ends), a run with fastx-toolkit can take almost a day or even more to accomplish, whereas seqtk requires a dozen or minutes or so

[Brian Bushnell]

It's also important to note what these tools can do, as per the original question. BBDuk does adapter-removal and quality-trimming in a single pass, faster than anything else; seqtk cannot perform adapter-removal.

Accuracy is also worth mentioning... since, in my opinion, it is generally more important than speed. BBDuk and seqtk have equal accuracy for quality-trimming, as they use the same algorithm. Anyway, that's a solved problem - the algorithm is optimal and cannot be improved. Everything else I've tested (which is everything commonly-used - trimmomatic, fastx, etc) is dramatically inferior, since it uses a non-optimal algorithm. Of course, quality-trimming is a dark art and often it's not even a good idea, but if you DO do it, you should do it correctly. Adapter-trimming, on the other hand, is ALWAYS a good idea (if done correctly).

BBDuk is the best adapter-trimming software available, by a huge margin. Let's put speed aside - it's the fastest, but that is never a good enough reason to use software unless more-accurate software is fundamentally too slow to use.

I have verified through extensive synthetic testing that BBDuk has a greater true-positive and lower false-positive rate of adapter-removal than anything else. In fact, those results were presented at AGBT a couple weeks ago. Maybe someone here attended?

In summary - I do not know of any useful read-trimming or read-filtering operation in which BBDuk is not the best tool in both accuracy and speed, aside from seqtk, which can exceed BBDuk's speed on single-ended reads.

Answer 7

[Lakshman Teja]

FASTP is really good to process FASTQ files and you can use the below command

fastp -i SRR098401_1.fastq.gz -I SRR098401_2.fastq.gz -o SRR098401_1_QC.fastq.gz -O SRR098401_2_QC.fastq.gz -g -x -p