cutPrimers: new tool for removing primer sequences from targeted NGS reads

[Sacrolfur]

I present you new tool for removing primer sequences from NGS reads that were obtained during sequencing amplicon-based targeted panel. You can download it from https://github.com/aakechin/cutPrimers. It runs under any OS: Linux, Mac OS, Windows. If you have any question, you can ask me.

Now, cutPrimers remove primer sequences only from unmapped reads in FASTQ-files. Later, it will be able to cut primer sequences also from mapped reads.

I will be glad to answer for any questions about its use.

[ankitgoyal]

Thanks for updating. Does this work on every windows version?

[Sacrolfur]

I tried it only on the Windows 7. Thank you for the question. I'll try it on the Windows XP and Windows 10

[ankitgoyal]

Thanks for replying. Please let me know once you get some results of trying it on other OS. I had to discuss this with my Boss.

[Sacrolfur]

I fixed some bugs for using in Windows. And I approved that it works now in Windows 7 and Windows 10. Windows XP will be a little bit later

[Sacrolfur]

Unfortunately, cutPrimers does not work in Windows XP, because in Windows XP you can not install Python 3.6 and can not install Biopython module, because you can not install Visual Studio C++

[garrulus glandarius]

When are you going to add a BAM processing option?

[Sacrolfur]

This can be done quickly and easily (I think during a week), but now I don't know how to efficiently read BAM-files in such a way that it will work in Windows. All exisiting Python modules need samtools that doesn't work in Windows. Maybe you know some variants or you can offer me some good algorithm?

[garrulus glandarius]

Thanks for the prompt reply.
Maybe you could add this option at least for Linux users?

[Sacrolfur]

Thanks for the prompt reply.
Maybe you could add this option at least for Linux users?

I'm not sure that I will be able to do it in this year (2017). Maybe in 2018. Why don't you want to use cutPrimers before mapping?

[garrulus glandarius]

Because, as far as I know, primer sequences aid in alignment process. Thanks for your answer.

[Sacrolfur]

Because, as far as I know, primer sequences aid in alignment process. Thanks for your answer.

It depends on the fragments that you study and the length of reads. In the most of cases, IMHO, sequence of amplicon without primers should be enough for good mapping.