Tool: Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
"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.
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Ram
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Malachi Griffith
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Malachi Griffith
2 answers
The authors have now put the source code in GitHub here.
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Malachi Griffith
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/
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note: there is no source code only binaries for linux
@Malachi, any reason only binaries are provided? Not that this is an open-source only forum, but we do skewer heavily towards that end.
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.
I was curious so I did a quick survey of the tools listed in the skewer publication:
The good news is that there are plenty of choices. Update: the authors have moved skewer into the open-source category.
Any time I run binary codes provided by untrusted sources I feel like playing Russian roulette -
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.
thanks for following up via email, looks like the authors will release it as a GitHub source code after all
Now we've deposited the source codes in https://github.com/relipmoc/skewer
Malachi, Thank you for pushing us to do the right thing!
Thank you for agreeing!
Cool, thanks for following up with the authors (and of course thanks to the authors for opening up the code)!