How to find a better performance NIPT analysis scripts ?

Question

[winter_li]

HI, I wanna find a NIPT pipeline ,but I do not which is better pipeline ? So can you recommend a complete pipeline scripts ?

thank you !!!

[User 59]

For what data source? Array? NGS? In what language? For what disorders?

[winter_li]

HI, data source is WGS data of next generation sequencing . R and Perl ,or python , better perl . T21，T13 and T18.

Thank you !

Answer 1

[Roy]

I'm the author of this set of scripts: https://github.com/rstraver/wisecondor

It seems rather popular and is used in several medical centres across the world for diagnostics on calling T13 T18 and T21. Feel free to ask questions on my work if you need help.

As for other works, I think RAPIDR is the most recent package I heard of in papers. I don't have a full list ready of alternative packages but most comparisons I've seen lately are between this and my work.

[User 59]

The OP has gone on to use RAPIDR according to more recent posts asking for further help, so an alternative may be welcome for them!

[winter_li]

HI , OP ? what's the full name of OP ?

[Roy]

OP is shorthand for Original Poster, which is you in this specific case, winter_li ;)

I also realised you went with RAPIDR from your posts (as Daniel Swan noted), after I submitted my response.

I see you asked a few more things now, but I'm not exactly hanging around on biostars on a daily basis, sorry for that. Happy to learn you found you could also ask through GitHub!

[winter_li]

thank you ,Roy, I will have a try .

[winter_li]

HI , I need to cut adapter sequence from single-end fastq of NIPT ? which tool should use ?

[milad eidi]

123Fastq has 2 approaches for trimming adapter contaminations. also have graphical user interface. https://sourceforge.net/projects/project-123ngs/