Tool:Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.

Question

[Malachi Griffith]

"This program implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences."

It provides a nice summary of its features compared to 15 other trimmer tools.

• Abstract in Pubmed
• Full text publication in BioMed Central
• Download from sourceforge (binaries)
• Download from github (source code)
• Discussion of the tool on SeqAnswers
• BioStar post discussion options for trimming paired end reads
• RNA-Seq Blog post about Skewer

[Istvan Albert]

note: there is no source code only binaries for linux

[Chris Fields]

@Malachi, any reason only binaries are provided? Not that this is an open-source only forum, but we do skewer heavily towards that end.

[Istvan Albert]

Any time I run binary codes provided by untrusted sources I feel like playing Russian roulette -

[Malachi Griffith]

I am not involved in the project, just read the paper and thought it sounded note worthy. I agree, would prefer open-source. Didn't notice that when I first posted it.

[Malachi Griffith]

I was curious so I did a quick survey of the tools listed in the skewer publication:

• OpenSource: AdapterRemoval, AlienTrimmer, SeqPrep, cutadapt, fastx_toolkit, nextclip, scythe, tagcleaner, trim_galore, trimmomatic, skewer
• Binaries only: SeqTrim, btrim, flexbar
• Unknown: 'EA-Tools'

The good news is that there are plenty of choices. Update: the authors have moved skewer into the open-source category.

[Malachi Griffith]

Agreed. Maybe the authors will see this lively discussion and put the source code up somewhere... I'll email the corresponding author, refer them to this thread and ask.

[Hongshan]

Now we've deposited the source codes in https://github.com/relipmoc/skewer

Malachi, Thank you for pushing us to do the right thing!

[Malachi Griffith]

Thank you for agreeing!

[Chris Fields]

Cool, thanks for following up with the authors (and of course thanks to the authors for opening up the code)!

[Istvan Albert]

thanks for following up via email, looks like the authors will release it as a GitHub source code after all

Answer 1

[Malachi Griffith]

The authors have now put the source code in GitHub here.

Answer 2

[anu014]

Doesn't this tool supports single-end data too? It claims "Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads" here : https://sourceforge.net/projects/skewer/